Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 123 of 259
Found at i:39803696 original size:228 final size:228
Alignment explanation
Indices: 39803299--39803725 Score: 854
Period size: 228 Copynumber: 1.9 Consensus size: 228
39803289 ATACATCATG
39803299 GCATTTAACATCACTTCATCATAATTTTACATCATGGCCGAATGCTCCTTTTAAACCATTTACCC
1 GCATTTAACATCACTTCATCATAATTTTACATCATGGCCGAATGCTCCTTTTAAACCATTTACCC
39803364 TCACAAAGCATAAATTTCACCATCAAACTTACAAGCTTATAATCCCATGAATTTTAACATCATAA
66 TCACAAAGCATAAATTTCACCATCAAACTTACAAGCTTATAATCCCATGAATTTTAACATCATAA
39803429 TATCTATCCAACTCTCACTCATTAACTTCTATCATAAATCTCAAAATCTATAGTTTTTCTACCCA
131 TATCTATCCAACTCTCACTCATTAACTTCTATCATAAATCTCAAAATCTATAGTTTTTCTACCCA
39803494 TGACAATTTAACAATATATACTCAATATTCAAA
196 TGACAATTTAACAATATATACTCAATATTCAAA
39803527 GCATTTAACATCACTTCATCATAATTTTACATCATGGCCGAATGCTCCTTTTAAACCATTTACCC
1 GCATTTAACATCACTTCATCATAATTTTACATCATGGCCGAATGCTCCTTTTAAACCATTTACCC
39803592 TCACAAAGCATAAATTTCACCATCAAACTTACAAGCTTATAATCCCATGAATTTTAACATCATAA
66 TCACAAAGCATAAATTTCACCATCAAACTTACAAGCTTATAATCCCATGAATTTTAACATCATAA
39803657 TATCTATCCAACTCTCACTCATTAACTTCTATCATAAATCTCAAAATCTATAGTTTTTCTACCCA
131 TATCTATCCAACTCTCACTCATTAACTTCTATCATAAATCTCAAAATCTATAGTTTTTCTACCCA
39803722 TGAC
196 TGAC
39803726 CGAAACCTCC
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
228 199 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (228 bp):
GCATTTAACATCACTTCATCATAATTTTACATCATGGCCGAATGCTCCTTTTAAACCATTTACCC
TCACAAAGCATAAATTTCACCATCAAACTTACAAGCTTATAATCCCATGAATTTTAACATCATAA
TATCTATCCAACTCTCACTCATTAACTTCTATCATAAATCTCAAAATCTATAGTTTTTCTACCCA
TGACAATTTAACAATATATACTCAATATTCAAA
Found at i:39807315 original size:55 final size:55
Alignment explanation
Indices: 39807221--39807335 Score: 194
Period size: 55 Copynumber: 2.1 Consensus size: 55
39807211 ACATTCATTC
* * *
39807221 ATCACAATTTAATATCAAATGAATAATAATTTAATTCAAACAGGCTTATTTGTAT
1 ATCAAAATTCAATATCAAATGAATAATAATTTAATTCAAACAAGCTTATTTGTAT
*
39807276 ATCAAAATTCAATATCAAATGGATAATAATTTAATTCAAACAAGCTTATTTGTAT
1 ATCAAAATTCAATATCAAATGAATAATAATTTAATTCAAACAAGCTTATTTGTAT
39807331 ATCAA
1 ATCAA
39807336 CTTACTTCAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (55 bp):
ATCAAAATTCAATATCAAATGAATAATAATTTAATTCAAACAAGCTTATTTGTAT
Found at i:39809709 original size:40 final size:40
Alignment explanation
Indices: 39809630--39809876 Score: 256
Period size: 40 Copynumber: 6.2 Consensus size: 40
39809620 CGGATGATAA
* * * * *
39809630 CCGGACTAAGATCTGAAGGCATTTGTGCGAGTTG-CTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * *
39809670 CCGGGCTATGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
39809710 CCGGGCTAAGACCCGAAGGCATTTGTG-TGAGTTACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCT-AGTGATTATAT
* * *
39809750 CCGGGCTATGTCCCGAAGGCATTTATG-TAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
39809789 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
*
39809829 CCGGGCTAAGACCCG-AGAGCATTTGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAG-GCATTTGTGCTAG-TGATTATAT
39809869 CC-GGCTAA
1 CCGGGCTAA
39809877 ATCTCGAAGA
Statistics
Matches: 178, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
39 44 0.25
40 132 0.74
41 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:39809885 original size:79 final size:80
Alignment explanation
Indices: 39809630--39809876 Score: 367
Period size: 79 Copynumber: 3.1 Consensus size: 80
39809620 CGGATGATAA
* * *
39809630 CCGGACTAAGATCTGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
39809695 TGCTAGTGATTATAT
66 TGCTAGTGATTATAT
* *
39809710 CCGGGCTAAGACCCGAAGGCATTTGTGTGAGTTACTATATCCGGGCTATGTCCCGAAGGCATTTA
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
39809775 TG-TAGTGATTATAT
66 TGCTAGTGATTATAT
* *
39809789 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCG-AGAGCATTT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAG-GCATTT
* *
39809853 GTGCGAGTTG-TTATAT
65 ATGCTAG-TGATTATAT
39809869 CC-GGCTAA
1 CCGGGCTAA
39809877 ATCTCGAAGA
Statistics
Matches: 153, Mismatches: 11, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
78 2 0.01
79 77 0.50
80 72 0.47
81 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
TGCTAGTGATTATAT
Found at i:39815430 original size:40 final size:40
Alignment explanation
Indices: 39815339--39815508 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
39815329 TCCTCGGTCA
* * * * *
39815339 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
39815378 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
39815418 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
39815458 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
39815498 AAGGCCTTCGG
1 AATGCCTTCGG
39815509 ATCTTAGTCC
Statistics
Matches: 112, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 32 0.29
40 80 0.71
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:39823288 original size:40 final size:40
Alignment explanation
Indices: 39823197--39823366 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 40
39823187 TCCTCGTTCA
* * * * *
39823197 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
39823236 CATGCCTTCGGGACGTAACCCGGATTTAACAACTTGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
39823276 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
39823316 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
39823356 AAGGCCTTCGG
1 AATGCCTTCGG
39823367 ATCTTAGTCC
Statistics
Matches: 110, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 31 0.28
40 79 0.72
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:39823298 original size:79 final size:80
Alignment explanation
Indices: 39823197--39823343 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 80
39823187 TCCTCGTTCA
* * * * *
39823197 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-CATGCCTTCGGGACGTAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGGAT
39823261 TTAACAACTTGCACG
66 TTAACAACTTGCACG
* * *
39823276 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCCTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGGAT
39823341 TTA
66 TTA
39823344 GTATCTCGCA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 34 0.58
80 25 0.42
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGGAT
TTAACAACTTGCACG
Found at i:39827448 original size:28 final size:29
Alignment explanation
Indices: 39827417--39827481 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
39827407 AAAGTAATTT
* *
39827417 TTGATAAAAATGTCAATT-AGGGATTAAA
1 TTGAGAAAAATGTAAATTGAGGGATTAAA
* *
39827445 TTGAGAAAAGTGTAAATTGAGGGGTTAAA
1 TTGAGAAAAATGTAAATTGAGGGATTAAA
*
39827474 TTGTGAAA
1 TTGAGAAA
39827482 TAAATGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.43, C:0.02, G:0.25, T:0.31
Consensus pattern (29 bp):
TTGAGAAAAATGTAAATTGAGGGATTAAA
Found at i:39829864 original size:13 final size:13
Alignment explanation
Indices: 39829846--39829870 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39829836 ACCAGGGGAC
39829846 ACATGACCGTGTA
1 ACATGACCGTGTA
39829859 ACATGACCGTGT
1 ACATGACCGTGT
39829871 GTTACACACG
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:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (13 bp):
ACATGACCGTGTA
Found at i:39831678 original size:14 final size:14
Alignment explanation
Indices: 39831635--39831685 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
39831625 AATATTTTAA
39831635 AATTTATTT-TGTG
1 AATTTATTTGTGTG
39831648 --TTTATTATGTGTG
1 AATTTATT-TGTGTG
*
39831661 AATTTATTTGTTTG
1 AATTTATTTGTGTG
39831675 AATTT-TTTGTG
1 AATTTATTTGTG
39831686 CTTTAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 6 0.19
12 1 0.03
13 9 0.28
14 10 0.31
15 6 0.19
ACGTcount: A:0.20, C:0.00, G:0.18, T:0.63
Consensus pattern (14 bp):
AATTTATTTGTGTG
Found at i:39836515 original size:23 final size:23
Alignment explanation
Indices: 39836489--39836538 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
39836479 TTACGTGAAG
*
39836489 TCAGTTTTCTGGGTCATGTTGTA
1 TCAGTTTTCTGGGCCATGTTGTA
39836512 TCAGTTTTCTGGGCCATGTTGTA
1 TCAGTTTTCTGGGCCATGTTGTA
39836535 TCAG
1 TCAG
39836539 CATCGGGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (23 bp):
TCAGTTTTCTGGGCCATGTTGTA
Found at i:39842932 original size:23 final size:23
Alignment explanation
Indices: 39842904--39842953 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
39842894 TTACGTGAAG
*
39842904 TCAGTTTTCTGGGTCATGTTGTA
1 TCAGTTTTCTGGGCCATGTTGTA
39842927 TCAGTTTTCTGGGCCATGTTGTA
1 TCAGTTTTCTGGGCCATGTTGTA
39842950 TCAG
1 TCAG
39842954 CATCGGGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (23 bp):
TCAGTTTTCTGGGCCATGTTGTA
Found at i:39850454 original size:27 final size:26
Alignment explanation
Indices: 39850415--39850525 Score: 123
Period size: 27 Copynumber: 4.1 Consensus size: 26
39850405 GGAAGCGTCT
*
39850415 TGGTGGCTATGCCACAATTATCTGATC
1 TGGTGGCTCTGCCAC-ATTATCTGATC
* *
39850442 TGGTGGCTCTGCCATATATATCTGTTC
1 TGGTGGCTCTGCCACAT-TATCTGATC
*
39850469 TGGTGGTTCTGCCACGATTATCTGTATC
1 TGGTGGCTCTGCCAC-ATTATCTG-ATC
* * *
39850497 TGGTGACTCTGTCACATTATCTGTTC
1 TGGTGGCTCTGCCACATTATCTGATC
39850523 TGG
1 TGG
39850526 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 7 0.10
27 48 0.68
28 16 0.23
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (26 bp):
TGGTGGCTCTGCCACATTATCTGATC
Found at i:39850518 original size:54 final size:54
Alignment explanation
Indices: 39850415--39850525 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
39850405 GGAAGCGTCT
* *
39850415 TGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCATATATATCTGTTC
1 TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTC
* * * *
39850469 TGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTTC
1 TGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTTC
39850523 TGG
1 TGG
39850526 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.66
55 17 0.34
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (54 bp):
TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTC
Found at i:39853568 original size:11 final size:11
Alignment explanation
Indices: 39853552--39853576 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39853542 GCTATAAAAA
39853552 ATTAAAATAAT
1 ATTAAAATAAT
39853563 ATTAAAATAAT
1 ATTAAAATAAT
39853574 ATT
1 ATT
39853577 TCAACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTAAAATAAT
Found at i:39855319 original size:37 final size:37
Alignment explanation
Indices: 39855261--39855331 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
39855251 GCTGAGACGA
*
39855261 AATCTCCACACGAAGTTATCGGGTCTTACCCGGACAT
1 AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAT
*
39855298 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACGAAGTCATCGGGTCTTACCCGGA
39855332 ATATATTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (37 bp):
AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAT
Found at i:39855517 original size:50 final size:51
Alignment explanation
Indices: 39855469--39855568 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 51
39855459 ACAATATACG
* *
39855469 CACATCGCCTGCATATTTCACACTAGCCATTCGGCTTTACCACATATACATA
1 CACATCGCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACA-A
* * *
39855521 CATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 CACATCGCATACATATTTCACACTAGCCATTCGGCTTTACCACATATA
39855569 TGCATGTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (51 bp):
CACATCGCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAA
Found at i:39855590 original size:47 final size:47
Alignment explanation
Indices: 39855538--39855684 Score: 204
Period size: 47 Copynumber: 3.1 Consensus size: 47
39855528 CATACATATT
* * * *
39855538 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
39855585 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
39855632 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
39855679 TCACAT
1 TCACAT
39855685 ACAATCCTAA
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 88 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:39861616 original size:19 final size:19
Alignment explanation
Indices: 39861594--39861690 Score: 79
Period size: 19 Copynumber: 5.2 Consensus size: 19
39861584 GCATAGTACT
*
39861594 TTTAGGCTCGCATAAAACA
1 TTTAAGCTCGCATAAAACA
* *
39861613 TTTAAGCTTGTATAAAACA
1 TTTAAGCTCGCATAAAACA
* ** *
39861632 TTT-GGCTCTTATAAAATA
1 TTTAAGCTCGCATAAAACA
* * * *
39861650 GTTAAGTTCACATGAAACA
1 TTTAAGCTCGCATAAAACA
*
39861669 ATTAAGCTCGCATAAAACA
1 TTTAAGCTCGCATAAAACA
39861688 TTT
1 TTT
39861691 GAAAGCAGGA
Statistics
Matches: 58, Mismatches: 19, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
18 13 0.22
19 45 0.78
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (19 bp):
TTTAAGCTCGCATAAAACA
Found at i:39861826 original size:22 final size:22
Alignment explanation
Indices: 39861798--39861849 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
39861788 AAGCTCACTC
**
39861798 ACTTTTATAGAGTTCGTACAAT
1 ACTTTTATAGAGTTCACACAAT
* *
39861820 ACTTTTATTGGGTTCACACAAT
1 ACTTTTATAGAGTTCACACAAT
39861842 ACTTTTAT
1 ACTTTTAT
39861850 TATGTTTGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (22 bp):
ACTTTTATAGAGTTCACACAAT
Found at i:39872154 original size:11 final size:11
Alignment explanation
Indices: 39872118--39872159 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
39872108 AAAATATTAC
39872118 TTTATTAATAT
1 TTTATTAATAT
*
39872129 TTTAATGAGATAT
1 TTT-ATTA-ATAT
39872142 TTTATTAATAT
1 TTTATTAATAT
39872153 TTTATTA
1 TTTATTA
39872160 TAAATAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.52
12 6 0.22
13 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TTTATTAATAT
Found at i:39878087 original size:39 final size:39
Alignment explanation
Indices: 39878032--39878212 Score: 254
Period size: 39 Copynumber: 4.6 Consensus size: 39
39878022 AACACAAATG
* *
39878032 CCTTCGGGACTTAGCCCAGATATAACACCTGCACGAATA
1 CCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATA
* *
39878071 CCTTCGGGACTAAGCCCGGATATAACACCAGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATA
* * * *
39878110 CCTTTGGGACTAAGCCCGGATATAACACCATCATGAATA
1 CCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATA
* * * *
39878149 CCTTTGAGACTTAGCCCAGATATAACACCAGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATA
39878188 CCTTCGGGACTTAGCCCGGATATAA
1 CCTTCGGGACTTAGCCCGGATATAA
39878213 ATCTCACACA
Statistics
Matches: 125, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 125 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATA
Found at i:39878165 original size:78 final size:78
Alignment explanation
Indices: 39878028--39878212 Score: 282
Period size: 78 Copynumber: 2.4 Consensus size: 78
39878018 TTCCAACACA
* * *
39878028 AATGCCTTCGGGACTTAGCCCAGATATAACACCTGCACGAATACCTTCGGGACTAAGCCCGGATA
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCTGCACGAATACCTTCGAGACTAAGCCCAGATA
39878093 TAACACCAGCACG
66 TAACACCAGCACG
* * * * *
39878106 AATGCCTTTGGGACTAAGCCCGGATATAACACCAT-CATGAATACCTTTGAGACTTAGCCCAGAT
1 AATGCCTTCGGGACTTAGCCCGGATATAACACC-TGCACGAATACCTTCGAGACTAAGCCCAGAT
39878170 ATAACACCAGCACG
65 ATAACACCAGCACG
39878184 AATGCCTTCGGGACTTAGCCCGGATATAA
1 AATGCCTTCGGGACTTAGCCCGGATATAA
39878213 ATCTCACACA
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
78 95 0.99
79 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (78 bp):
AATGCCTTCGGGACTTAGCCCGGATATAACACCTGCACGAATACCTTCGAGACTAAGCCCAGATA
TAACACCAGCACG
Found at i:39885690 original size:19 final size:20
Alignment explanation
Indices: 39885666--39885703 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39885656 GGTACCACCA
39885666 AAACAT-ATATCAT-ATCTTT
1 AAACATCAT-TCATCATCTTT
39885685 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
39885704 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:39886044 original size:93 final size:93
Alignment explanation
Indices: 39885933--39886103 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
39885923 GCCTCTAAGT
* * *
39885933 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
39885998 CAAGTTCAGATGCCTAGTTACATCTCAC
66 CAAGTTCAGATGCCTAGTTACATCTCAC
* * * *
39886026 GAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
* *
39886091 CGAGTTCGGATGC
66 CAAGTTCAGATGC
39886104 TCAACCATCC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
CAAGTTCAGATGCCTAGTTACATCTCAC
Found at i:39886092 original size:46 final size:46
Alignment explanation
Indices: 39885928--39886100 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
39885918 AACCTGCCTC
* * * * **
39885928 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
* * * *
39885974 TAAATGAACTCGGACTCAACTCAACAAGTTCAGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-G--GAC-ATTTACATCCA
* *
39886022 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
39886067 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39886101 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 7 0.07
44 3 0.03
45 2 0.02
46 57 0.55
47 26 0.25
48 2 0.02
49 3 0.03
50 4 0.04
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
Found at i:39891119 original size:23 final size:23
Alignment explanation
Indices: 39891093--39891136 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
39891083 CGCAAAAATA
* *
39891093 ATTAAATGTTAAATTTCATGTCT
1 ATTAAATGTGAAATTACATGTCT
*
39891116 ATTATATGTGAAATTACATGT
1 ATTAAATGTGAAATTACATGT
39891137 GTGAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (23 bp):
ATTAAATGTGAAATTACATGTCT
Found at i:39895711 original size:39 final size:39
Alignment explanation
Indices: 39895657--39895734 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
39895647 CTAGAACATA
39895657 CCTTGAATCAAGCTTGAGAACAACCGAACCTAGGTTTTC
1 CCTTGAATCAAGCTTGAGAACAACCGAACCTAGGTTTTC
39895696 CCTTGAATCAAGCTTGAGAACAACCGAACCTAGGTTTTC
1 CCTTGAATCAAGCTTGAGAACAACCGAACCTAGGTTTTC
39895735 TTTCTCTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (39 bp):
CCTTGAATCAAGCTTGAGAACAACCGAACCTAGGTTTTC
Found at i:39897923 original size:13 final size:13
Alignment explanation
Indices: 39897905--39897929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39897895 CGTGTGTAAC
39897905 ACACGGTCATGTT
1 ACACGGTCATGTT
39897918 ACACGGTCATGT
1 ACACGGTCATGT
39897930 GTCCCCTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (13 bp):
ACACGGTCATGTT
Found at i:39910480 original size:12 final size:12
Alignment explanation
Indices: 39910463--39910488 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39910453 TAGTTAAATG
39910463 AACTAAAAGACA
1 AACTAAAAGACA
39910475 AACTAAAAGACA
1 AACTAAAAGACA
39910487 AA
1 AA
39910489 ATTTTTCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.15, G:0.08, T:0.08
Consensus pattern (12 bp):
AACTAAAAGACA
Found at i:39941404 original size:43 final size:42
Alignment explanation
Indices: 39941263--39941426 Score: 215
Period size: 42 Copynumber: 3.9 Consensus size: 42
39941253 TTAGGGTTAC
39941263 TGAGATTACGTGTAAGACCATATCTAGGATATGGCATCGATA
1 TGAGATTACGTGTAAGACCATATCTAGGATATGGCATCGATA
*
39941305 TGAGATTTCGTGTAAGACCATATCTAGGATATGGCATCGATA
1 TGAGATTACGTGTAAGACCATATCTAGGATATGGCATCGATA
* * *
39941347 TGAGACTT-TGTGTAAGACCATAGT-TGGGCTATTGGCATCGATA
1 TGAGA-TTACGTGTAAGACCATA-TCTAGGATA-TGGCATCGATA
* * * *
39941390 CGAGATTACATGTAAGACCATATCTGGGATATTGCAT
1 TGAGATTACGTGTAAGACCATATCTAGGATATGGCAT
39941427 TGGTACGGTA
Statistics
Matches: 108, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
42 72 0.67
43 36 0.33
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (42 bp):
TGAGATTACGTGTAAGACCATATCTAGGATATGGCATCGATA
Found at i:39941405 original size:85 final size:84
Alignment explanation
Indices: 39941272--39941426 Score: 222
Period size: 85 Copynumber: 1.8 Consensus size: 84
39941262 CTGAGATTAC
* * *
39941272 GTGTAAGACCATATCTAGGATATGGCATCGATATGAGATTTCGTGTAAGACCATATCTAGGATAT
1 GTGTAAGACCATATCTAGGATATGGCATCGATACGAGATTACATGTAAGACCATATCTAGGATAT
39941337 GGCATCGATATGAGACTTT
66 GGCATCGATATGAGACTTT
* * *
39941356 GTGTAAGACCATAGT-TGGGCTATTGGCATCGATACGAGATTACATGTAAGACCATATCTGGGAT
1 GTGTAAGACCATA-TCTAGGATA-TGGCATCGATACGAGATTACATGTAAGACCATATCTAGGAT
*
39941420 ATTGCAT
64 ATGGCAT
39941427 TGGTACGGTA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 18 0.29
85 44 0.71
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (84 bp):
GTGTAAGACCATATCTAGGATATGGCATCGATACGAGATTACATGTAAGACCATATCTAGGATAT
GGCATCGATATGAGACTTT
Found at i:39944281 original size:28 final size:29
Alignment explanation
Indices: 39944172--39944285 Score: 135
Period size: 29 Copynumber: 4.0 Consensus size: 29
39944162 TGAGCATGAT
* *
39944172 TATGAATGTGA-TTGGGCCTCACGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
* *
39944200 AATAAATGTGATTTGGGCCTAATGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
*
39944229 TAT-ACAAGTGATTTGGGCCTAATGGGCCA
1 TATGA-ATGTGATTTGGGCCTAATGGGCCA
* *
39944258 TATGAATCTGA-TTGGGCTTAATGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
39944286 GATACAGGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
28 26 0.35
29 47 0.64
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (29 bp):
TATGAATGTGATTTGGGCCTAATGGGCCA
Found at i:39944281 original size:57 final size:57
Alignment explanation
Indices: 39944179--39944291 Score: 147
Period size: 57 Copynumber: 2.0 Consensus size: 57
39944169 GATTATGAAT
* * *
39944179 GTGATTGGGCCTCACGGGCCAAATAAATGTGATTTGGGCCTAATGGGCCATATACAA
1 GTGATTGGGCCTAACGGGCCAAATAAATCTGATTTGGGCCTAATGGGCCAGATACAA
* * * *
39944236 GTGATTTGGGCCTAATGGGCCATATGAATCTGA-TTGGGCTTAATGGGCCAGATACA
1 GTGA-TTGGGCCTAACGGGCCAAATAAATCTGATTTGGGCCTAATGGGCCAGATACA
39944292 GGTATGTGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 25 0.52
58 23 0.48
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (57 bp):
GTGATTGGGCCTAACGGGCCAAATAAATCTGATTTGGGCCTAATGGGCCAGATACAA
Found at i:39947130 original size:25 final size:24
Alignment explanation
Indices: 39947083--39947139 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
39947073 AGTTAGTAAT
*
39947083 AAAGAAATGGAGAAAAAAAAAAGA
1 AAAGAAAAGGAGAAAAAAAAAAGA
*
39947107 GAAAGAAAAGGATG-AAAACAAAAGA
1 -AAAGAAAAGGA-GAAAAAAAAAAGA
*
39947132 AAAAAAAA
1 AAAGAAAA
39947140 TGTGTCCATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 7 0.25
25 20 0.71
26 1 0.04
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (24 bp):
AAAGAAAAGGAGAAAAAAAAAAGA
Found at i:39948584 original size:40 final size:41
Alignment explanation
Indices: 39948386--39948570 Score: 195
Period size: 40 Copynumber: 4.6 Consensus size: 41
39948376 TCGAATGATG
* * *
39948386 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * * * *
39948426 TCCAGACTAAGAT-CCGAAGGCATTTGTACGAGATACTA-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
39948466 TTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39948505 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39948546 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39948571 AACGAGTAGC
Statistics
Matches: 119, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 32 0.27
40 78 0.66
41 9 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:39948593 original size:79 final size:79
Alignment explanation
Indices: 39948439--39948593 Score: 172
Period size: 79 Copynumber: 2.0 Consensus size: 79
39948429 AGACTAAGAT
** **
39948439 CCGAAGGCATTTGTACGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTACGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
39948504 ATCCGGGTTAAGTC
66 ATCCGAGTTAAGTC
* * * *
39948518 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTACGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
39948581 TATATCC-AGTTAA
63 TAAATCCGAGTTAA
39948594 ATTCCAAAGG
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
78 2 0.03
79 37 0.59
80 24 0.38
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTACGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGAGTTAAGTC
Found at i:39956621 original size:40 final size:41
Alignment explanation
Indices: 39956423--39956607 Score: 213
Period size: 40 Copynumber: 4.6 Consensus size: 41
39956413 TCGAATGATG
* * * *
39956423 TCCGGGCTAAGTCCCGAAGGC-TTTGTCCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
39956463 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39956503 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39956542 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39956583 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39956608 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 34 0.27
40 81 0.65
41 9 0.07
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:39961539 original size:42 final size:42
Alignment explanation
Indices: 39961491--39961652 Score: 229
Period size: 42 Copynumber: 3.9 Consensus size: 42
39961481 TTAGGGTTAC
*
39961491 TGAGATTACGTGTAAGACCATATCTGGGATATGACATCGATA
1 TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
*
39961533 TGAGATTTA-GTGTAAGACCATATCTGGGATATGGCATGGATA
1 TGAGA-TTACGTGTAAGACCATATCTGGGATATGGCATCGATA
* * *
39961575 TGAGACT-CGTGTAAGACCATAACTGGGTTATTGGCATCGATA
1 TGAGATTACGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* *
39961617 CGAGATTACATGTAAGACCATATCTGGGATATGGCA
1 TGAGATTACGTGTAAGACCATATCTGGGATATGGCA
39961653 CTGGTACGGC
Statistics
Matches: 105, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
41 21 0.20
42 61 0.58
43 23 0.22
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.28
Consensus pattern (42 bp):
TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:39964687 original size:44 final size:43
Alignment explanation
Indices: 39964583--39964727 Score: 220
Period size: 43 Copynumber: 3.4 Consensus size: 43
39964573 GTTACTGAGG
* *
39964583 TTTCGTATAAGACCATATCTAGGATATGGCATCGGTATGTGAT
1 TTTCGTATAAGACCATATCTGGGAAATGGCATCGGTATGTGAT
39964626 TTTCGTATAAGACCATATCTGGGAAATGGCATCGGTATGTGAAT
1 TTTCGTATAAGACCATATCTGGGAAATGGCATCGGTATGTG-AT
* * * *
39964670 TTTCTTATAAGACCATATTTGGGAAATGGAATCAGTATGTGA-
1 TTTCGTATAAGACCATATCTGGGAAATGGCATCGGTATGTGAT
39964712 TTTCGTATAAGACCAT
1 TTTCGTATAAGACCAT
39964728 GTCAGAGACA
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
42 15 0.16
43 40 0.43
44 39 0.41
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (43 bp):
TTTCGTATAAGACCATATCTGGGAAATGGCATCGGTATGTGAT
Found at i:39967985 original size:44 final size:43
Alignment explanation
Indices: 39967881--39968025 Score: 220
Period size: 43 Copynumber: 3.4 Consensus size: 43
39967871 GTTACTGAGG
* *
39967881 TTTCGTATAAGACCATATCTAGGATATGGCATCGGTATGTGAT
1 TTTCGTATAAGACCATATCTGGGAAATGGCATCGGTATGTGAT
39967924 TTTCGTATAAGACCATATCTGGGAAATGGCATCGGTATGTGAAT
1 TTTCGTATAAGACCATATCTGGGAAATGGCATCGGTATGTG-AT
* * * *
39967968 TTTCTTATAAGACCATATTTGGGAAATGGAATCAGTATGTGA-
1 TTTCGTATAAGACCATATCTGGGAAATGGCATCGGTATGTGAT
39968010 TTTCGTATAAGACCAT
1 TTTCGTATAAGACCAT
39968026 GTCAGAGACA
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
42 15 0.16
43 40 0.43
44 39 0.41
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (43 bp):
TTTCGTATAAGACCATATCTGGGAAATGGCATCGGTATGTGAT
Found at i:39969141 original size:3 final size:3
Alignment explanation
Indices: 39969133--39969186 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
39969123 AGTAGATTTA
* * * * *
39969133 ATT ATT ATT ATT AGT AGT AGT ATT ATA ACT A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39969180 ATT ATT A
1 ATT ATT A
39969187 AATAAATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:39970369 original size:15 final size:14
Alignment explanation
Indices: 39970348--39970394 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
39970338 ATTACTATAA
39970348 TTTAAGTTATTTAT
1 TTTAAGTTATTTAT
*
39970362 TATTAAG-TATTAAT
1 T-TTAAGTTATTTAT
*
39970376 TTTAAATTTATTTAT
1 TTT-AAGTTATTTAT
39970391 TTTA
1 TTTA
39970395 TAGTAAGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 2 0.07
14 11 0.41
15 14 0.52
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (14 bp):
TTTAAGTTATTTAT
Found at i:39991958 original size:13 final size:13
Alignment explanation
Indices: 39991938--39991970 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39991928 TTACCATTAA
39991938 TTTT-TTTTTATT
1 TTTTATTTTTATT
39991950 TTTTATTTTTATT
1 TTTTATTTTTATT
*
39991963 TTTAATTT
1 TTTTATTT
39991971 AGGGATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:39992795 original size:41 final size:41
Alignment explanation
Indices: 39992738--39992819 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
39992728 TACGAAAGTG
39992738 CATTCAAACTTGGAGGACTGCAGGTTTTT-CCTGTTATTGTT
1 CATTCAAACTTGGAGGACTGCA-GTTTTTCCCTGTTATTGTT
39992779 CATTCAAACTTGGAGGACTGCAGTTTTTCCCTGTTATTGTT
1 CATTCAAACTTGGAGGACTGCAGTTTTTCCCTGTTATTGTT
39992820 TTTCCATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 6 0.15
41 34 0.85
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (41 bp):
CATTCAAACTTGGAGGACTGCAGTTTTTCCCTGTTATTGTT
Found at i:39993006 original size:36 final size:36
Alignment explanation
Indices: 39992948--39993173 Score: 301
Period size: 36 Copynumber: 6.3 Consensus size: 36
39992938 TAAGAATTTT
* * *
39992948 TATTTTAAAAATACAAATGATTGCATTAGGTTTAAAA
1 TATTTT-AAATTAAAAATGATTGCATTAGGTATAAAA
* *
39992985 TATTTTAAATTAAAAATGATTGTATTAGGAATAAAA
1 TATTTTAAATTAAAAATGATTGCATTAGGTATAAAA
* * **
39993021 TATTTTAAATTAAAATTGATTGTATTAGGTATAAGG
1 TATTTTAAATTAAAAATGATTGCATTAGGTATAAAA
* *
39993057 TATTTTAAATTAAATATGATTGCAATAGGTATAAAA
1 TATTTTAAATTAAAAATGATTGCATTAGGTATAAAA
* *
39993093 TATTTTAAATTAATAATGATTGCATTAAGTATAAAA
1 TATTTTAAATTAAAAATGATTGCATTAGGTATAAAA
**
39993129 TATTTTAAATTAAAAAT-ATTGTGTTAGGTATAAAA
1 TATTTTAAATTAAAAATGATTGCATTAGGTATAAAA
39993164 TATTTTAAAT
1 TATTTTAAAT
39993174 CAATTTATAA
Statistics
Matches: 166, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
35 25 0.15
36 135 0.81
37 6 0.04
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.42
Consensus pattern (36 bp):
TATTTTAAATTAAAAATGATTGCATTAGGTATAAAA
Found at i:39993144 original size:16 final size:16
Alignment explanation
Indices: 39993089--39993148 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
39993079 CAATAGGTAT
39993089 AAAATATTTTAAATTA
1 AAAATATTTTAAATTA
* *
39993105 ATAATGATTGCATT-AAGTA
1 AAAAT-ATT---TTAAATTA
39993124 TAAAATATTTTAAATTA
1 -AAAATATTTTAAATTA
39993141 AAAATATT
1 AAAATATT
39993149 GTGTTAGGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
16 14 0.41
17 7 0.21
19 7 0.21
20 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (16 bp):
AAAATATTTTAAATTA
Found at i:39993524 original size:18 final size:16
Alignment explanation
Indices: 39993501--39993573 Score: 58
Period size: 18 Copynumber: 4.4 Consensus size: 16
39993491 GTTTTAGATT
39993501 TTTTTTTCAAATTTTATA
1 TTTTTTT-AAATTTTA-A
* *
39993519 TTTTTTTAAAATATAA
1 TTTTTTTAAATTTTAA
39993535 TTTTTTTAAAATTTATAA
1 TTTTTTT-AAATTT-TAA
* * *
39993553 ATTTTTT-ATTTTTTA
1 TTTTTTTAAATTTTAA
39993568 TTTTTT
1 TTTTTT
39993574 ATTTTTGAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
15 7 0.16
16 12 0.27
17 10 0.22
18 16 0.36
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTTTAAATTTTAA
Found at i:39993537 original size:16 final size:17
Alignment explanation
Indices: 39993501--39993560 Score: 68
Period size: 18 Copynumber: 3.5 Consensus size: 17
39993491 GTTTTAGATT
* *
39993501 TTTTTTTCAAATTTTATA
1 TTTTTTTAAAATTATA-A
39993519 TTTTTTTAAAA-TATAA
1 TTTTTTTAAAATTATAA
39993535 TTTTTTTAAAATTTATAA
1 TTTTTTTAAAA-TTATAA
*
39993553 ATTTTTTA
1 TTTTTTTA
39993561 TTTTTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 12 0.32
17 3 0.08
18 22 0.59
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTTTAAAATTATAA
Found at i:39993571 original size:6 final size:7
Alignment explanation
Indices: 39993553--39993579 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
39993543 AAATTTATAA
39993553 ATTTTTT
1 ATTTTTT
39993560 ATTTTTT
1 ATTTTTT
39993567 ATTTTTT
1 ATTTTTT
39993574 ATTTTT
1 ATTTTT
39993580 GAAAATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:39995193 original size:23 final size:23
Alignment explanation
Indices: 39995164--39995217 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
39995154 ACCCCACATG
*
39995164 GTGTGTAGGGATGGTCGGAGATT
1 GTGTGTAGGGATGGTCAGAGATT
39995187 GTGTGTAGGGATGGTCAGAGATT
1 GTGTGTAGGGATGGTCAGAGATT
39995210 GTGTGTAG
1 GTGTGTAG
39995218 AGGCTGGCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.04, G:0.46, T:0.31
Consensus pattern (23 bp):
GTGTGTAGGGATGGTCAGAGATT
Found at i:39999290 original size:46 final size:46
Alignment explanation
Indices: 39999220--39999392 Score: 167
Period size: 46 Copynumber: 3.7 Consensus size: 46
39999210 TTGGGCATCT
*
39999220 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
1 GAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* * *
39999266 GAACTCATTGAGTTGAGTCTGAGTTCA-TGA--GATG-TAACTAGGCATCC
1 GAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G--TCC
* * * *
39999313 GAGCTCTTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCC
1 GAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* *
39999359 GAGCT-AGTTGAGTTGAGTCCGAGTTGACTTATGG
1 GAACTCA-TTGAGTTGAGTCCGAGTTCACTTATGG
39999393 GTGGGTTACA
Statistics
Matches: 104, Mismatches: 13, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 58 0.56
47 27 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (46 bp):
GAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
Found at i:39999372 original size:93 final size:93
Alignment explanation
Indices: 39999213--39999383 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
39999203 CGGATATTTG
* *
39999213 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
*
39999278 TTGAGTCTGAGTTCATGAGATGTAACTA
66 TTGAGTCCGAGTTCATGAGATGTAACTA
* * * *
39999306 GGCATCCGAGCTCTTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCT-AGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCA-TTGA
39999370 GTTGAGTCCGAGTT
65 GTTGAGTCCGAGTT
39999384 GACTTATGGG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
92 1 0.01
93 69 0.99
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
TTGAGTCCGAGTTCATGAGATGTAACTA
Found at i:40001931 original size:46 final size:48
Alignment explanation
Indices: 40001859--40001961 Score: 147
Period size: 46 Copynumber: 2.2 Consensus size: 48
40001849 GACAGGACAG
* * * *
40001859 GACAGAAATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
*
40001905 GACAGGAATGAGCCATGTAAGCCCATATTATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
40001953 GACAGGAAT
1 GACAGGAAT
40001962 AATTTATGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 27 0.54
47 1 0.02
48 22 0.44
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
Found at i:40003244 original size:23 final size:23
Alignment explanation
Indices: 40003218--40003261 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
40003208 GGTGACGGTT
* *
40003218 TCGAGCGTGGGGGTGTTACAGTC
1 TCGAGCATGGGGGCGTTACAGTC
*
40003241 TCGAGTATGGGGGCGTTACAG
1 TCGAGCATGGGGGCGTTACAG
40003262 AAAGAGGGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.43, T:0.25
Consensus pattern (23 bp):
TCGAGCATGGGGGCGTTACAGTC
Found at i:40004196 original size:29 final size:29
Alignment explanation
Indices: 40004118--40004261 Score: 206
Period size: 29 Copynumber: 5.1 Consensus size: 29
40004108 CACATACCTG
* *
40004118 TATATGGCCCACTAGGCCC-AATCTC-TT
1 TATATGGCCCATTAGGCCCAAATCACATT
*
40004145 TCATATGGCCCA-GAGGCCCAAATCACATT
1 T-ATATGGCCCATTAGGCCCAAATCACATT
40004174 TATATGGCCCATTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
*
40004203 TATATGGACCATTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
*
40004232 CATATGG-CCATTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
40004260 TA
1 TA
40004262 CAGTCACGCT
Statistics
Matches: 107, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
27 7 0.07
28 47 0.44
29 53 0.50
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATCACATT
Found at i:40004250 original size:57 final size:57
Alignment explanation
Indices: 40004119--40004261 Score: 202
Period size: 57 Copynumber: 2.5 Consensus size: 57
40004109 ACATACCTGT
* * * *
40004119 ATATGGCCCACTAGGCCC-AATCTC-TTTCATATGGCCCAGAGGCCCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAATCACATTT-ATATGGACCAGAGGCCCAAATCACATTC
*
40004175 ATATGGCCCATTAGGCCCAAATCACATTTATATGGACCATTAGGCCCAAATCACATTC
1 ATATGGCCCATTAGGCCCAAATCACATTTATATGGACCA-GAGGCCCAAATCACATTC
40004233 ATATGG-CCATTAGGCCCAAATCACATTTA
1 ATATGGCCCATTAGGCCCAAATCACATTTA
40004262 CAGTCACGCT
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
56 17 0.22
57 37 0.47
58 25 0.32
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.26
Consensus pattern (57 bp):
ATATGGCCCATTAGGCCCAAATCACATTTATATGGACCAGAGGCCCAAATCACATTC
Found at i:40005265 original size:40 final size:40
Alignment explanation
Indices: 40005210--40005289 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
40005200 AAGAAAAGAA
40005210 GAGATGGTACACGACTGAAGCACACAAAAACAACAAATGC
1 GAGATGGTACACGACTGAAGCACACAAAAACAACAAATGC
40005250 GAGATGGTACACGACTGAAGCACACAAAAACAACAAATGC
1 GAGATGGTACACGACTGAAGCACACAAAAACAACAAATGC
40005290 CCTTACTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (40 bp):
GAGATGGTACACGACTGAAGCACACAAAAACAACAAATGC
Found at i:40011940 original size:25 final size:26
Alignment explanation
Indices: 40011903--40011969 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 26
40011893 TATTATTTAC
* *
40011903 AAAAATAATTATAT-TAATTTAATAA
1 AAAAATAAATATATATAATTGAATAA
40011928 AAAAATAAATATATATATAATTGAATAA
1 AAAAAT-AA-ATATATATAATTGAATAA
*
40011956 AAATA-AAATATATA
1 AAAAATAAATATATA
40011970 AAAGATAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 13 0.36
26 4 0.11
27 5 0.14
28 14 0.39
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (26 bp):
AAAAATAAATATATATAATTGAATAA
Found at i:40011957 original size:27 final size:27
Alignment explanation
Indices: 40011903--40011969 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 27
40011893 TATTATTTAC
*
40011903 AAAAAT-AAT-TATAT-TAATTTAATAA
1 AAAAATAAATATATATATAATTGAAT-A
40011928 AAAAATAAATATATATATAATTGAAT-
1 AAAAATAAATATATATATAATTGAATA
40011954 AAAAATAAA-ATATATA
1 AAAAATAAATATATATA
40011970 AAAGATAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
25 13 0.34
26 12 0.32
27 5 0.13
28 8 0.21
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (27 bp):
AAAAATAAATATATATATAATTGAATA
Found at i:40011979 original size:25 final size:25
Alignment explanation
Indices: 40011923--40011979 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
40011913 ATATTAATTT
*
40011923 AATAA-AAAAATAAATATATATATA
1 AATAATAAAAATAAATATATATAAA
*
40011947 ATTGAATAAAAATAAA-ATATATAAA
1 AAT-AATAAAAATAAATATATATAAA
40011972 AGATAATA
1 A-ATAATA
40011980 TTAGTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 2 0.07
25 15 0.56
26 10 0.37
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (25 bp):
AATAATAAAAATAAATATATATAAA
Found at i:40014845 original size:27 final size:27
Alignment explanation
Indices: 40014815--40014992 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40014805 ATATTGAGTC
* * * *
40014815 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40014842 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40014869 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40014897 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40014924 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40014951 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40014978 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40014993 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40014954 original size:82 final size:81
Alignment explanation
Indices: 40014836--40014991 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40014826 TGCTATATAA
* *
40014836 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40014901 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40014918 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40014982 CACTTAGTGC
65 CACTTAGTGC
40014992 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40030053 original size:12 final size:12
Alignment explanation
Indices: 40030036--40030060 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40030026 AAAATAGGGC
40030036 TTTAGTGGCGTT
1 TTTAGTGGCGTT
40030048 TTTAGTGGCGTT
1 TTTAGTGGCGTT
40030060 T
1 T
40030061 GGACAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.32, T:0.52
Consensus pattern (12 bp):
TTTAGTGGCGTT
Found at i:40030163 original size:41 final size:41
Alignment explanation
Indices: 40030117--40030438 Score: 403
Period size: 41 Copynumber: 7.9 Consensus size: 41
40030107 AAACGCCGTA
* *
40030117 AAAAACTGAGCAATAGCTGCGTTTTTGGTCCAAACACCACT
1 AAAAACTGAGCAATAGCGGCGTTTTTGGTCCAAACGCCACT
* * *
40030158 AAAAACTGAGCAATAGCGGCGTTTTTGGTCTAAATGCC-GT
1 AAAAACTGAGCAATAGCGGCGTTTTTGGTCCAAACGCCACT
**
40030198 AAAAAACTGAGCAATAGCGGCGTTTTTACTCCAAACGCCACT
1 -AAAAACTGAGCAATAGCGGCGTTTTTGGTCCAAACGCCACT
* *
40030240 AAAAATTGAGCAATAGCGGCGTTTTTGGTTCAAACGCCACT
1 AAAAACTGAGCAATAGCGGCGTTTTTGGTCCAAACGCCACT
* * * **
40030281 AAAAACTGAGCAATAGCGGCGTTTCTAGTTCAAACGCTGCT
1 AAAAACTGAGCAATAGCGGCGTTTTTGGTCCAAACGCCACT
* * * * *
40030322 AAAAACTGAGCAATAGCGGCGTTTCTAGTTCAAATGCCGCT
1 AAAAACTGAGCAATAGCGGCGTTTTTGGTCCAAACGCCACT
* *
40030363 AAAAACTGAGCAATAGTGGCATTTTTGGTCCAAACGCCACT
1 AAAAACTGAGCAATAGCGGCGTTTTTGGTCCAAACGCCACT
* * * *
40030404 AAAAACTAAGCAATAGTGGTGTTTCTGGTCCAAAC
1 AAAAACTGAGCAATAGCGGCGTTTTTGGTCCAAAC
40030439 ACTGTAAAAA
Statistics
Matches: 247, Mismatches: 32, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
40 1 0.00
41 245 0.99
42 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.25
Consensus pattern (41 bp):
AAAAACTGAGCAATAGCGGCGTTTTTGGTCCAAACGCCACT
Found at i:40030456 original size:123 final size:122
Alignment explanation
Indices: 40030117--40030448 Score: 450
Period size: 123 Copynumber: 2.7 Consensus size: 122
40030107 AAACGCCGTA
*
40030117 AAAAACTGAGCAATAGCT-GCGTTTTTGGTCCAAACACCACTAAAAACTGAGCAATAGCGGCGTT
1 AAAAACTGAGCAATAG-TGGCGTTTTTGGTCCAAACGCCACTAAAAACTGAGCAATAGCGGCGTT
* * * * *
40030181 TTTGGTCTAAATGCCGTAAAAAACTGAGCAATAGCGGCGTTTTTACTCCAAACGCCACT
65 TCTGGTCCAAACGCTGT-AAAAACTGAGCAATAGCGGCGTTTCTACTCCAAACGCCACT
* * *
40030240 AAAAATTGAGCAATAGCGGCGTTTTTGGTTCAAACGCCACTAAAAACTGAGCAATAGCGGCGTTT
1 AAAAACTGAGCAATAGTGGCGTTTTTGGTCCAAACGCCACTAAAAACTGAGCAATAGCGGCGTTT
* * * * * *
40030305 CTAGTTCAAACGCTGCTAAAAACTGAGCAATAGCGGCGTTTCTAGTTCAAATGCCGCT
66 CTGGTCCAAACGCTG-TAAAAACTGAGCAATAGCGGCGTTTCTACTCCAAACGCCACT
* * * *
40030363 AAAAACTGAGCAATAGTGGCATTTTTGGTCCAAACGCCACTAAAAACTAAGCAATAGTGGTGTTT
1 AAAAACTGAGCAATAGTGGCGTTTTTGGTCCAAACGCCACTAAAAACTGAGCAATAGCGGCGTTT
*
40030428 CTGGTCCAAACACTGTAAAAA
66 CTGGTCCAAACGCTGTAAAAA
40030449 GTTGAGCAGC
Statistics
Matches: 182, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
122 6 0.03
123 175 0.96
124 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (122 bp):
AAAAACTGAGCAATAGTGGCGTTTTTGGTCCAAACGCCACTAAAAACTGAGCAATAGCGGCGTTT
CTGGTCCAAACGCTGTAAAAACTGAGCAATAGCGGCGTTTCTACTCCAAACGCCACT
Found at i:40030784 original size:7 final size:7
Alignment explanation
Indices: 40030724--40030789 Score: 60
Period size: 7 Copynumber: 9.1 Consensus size: 7
40030714 CTTTCTCTAT
40030724 ACCCTAA
1 ACCCTAA
*
40030731 ACCTTAA
1 ACCCTAA
*
40030738 ACCTTAA
1 ACCCTAA
40030745 ACCCTAA
1 ACCCTAA
*
40030752 ACACTAA
1 ACCCTAA
* *
40030759 TCCATAA
1 ACCCTAA
*
40030766 ACCCCAAA
1 A-CCCTAA
40030774 ACCCTAA
1 ACCCTAA
40030781 ACCCCTAA
1 A-CCCTAA
40030789 A
1 A
40030790 AAATTCATAT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
7 35 0.74
8 12 0.26
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (7 bp):
ACCCTAA
Found at i:40031007 original size:21 final size:21
Alignment explanation
Indices: 40030967--40031007 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40030957 TTAAGTTTAT
*
40030967 GGTTTAGGGTTTGTTATTTTG
1 GGTTTAGGGTTTATTATTTTG
*
40030988 GGTTTAGGGTTTATTGTTTT
1 GGTTTAGGGTTTATTATTTT
40031008 AAAGTTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.32, T:0.59
Consensus pattern (21 bp):
GGTTTAGGGTTTATTATTTTG
Found at i:40031063 original size:22 final size:21
Alignment explanation
Indices: 40031018--40031064 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
40031008 AAAGTTTGTT
*
40031018 GTTTGGGGTTTAATGTTTAAG
1 GTTTAGGGTTTAATGTTTAAG
* *
40031039 GTTTAGGGTCTTAGTGTTTATG
1 GTTTAGGGT-TTAATGTTTAAG
40031061 GTTT
1 GTTT
40031065 TAAGGGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.15, C:0.02, G:0.32, T:0.51
Consensus pattern (21 bp):
GTTTAGGGTTTAATGTTTAAG
Found at i:40033339 original size:27 final size:27
Alignment explanation
Indices: 40033272--40033333 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
40033262 TGAACTAAAA
**
40033272 TTATAATTTAAAAATAAGATCTACTTT
1 TTATAATAAAAAAATAAGATCTACTTT
40033299 TTATAATAAAAAAATAAGATCTACTTT
1 TTATAATAAAAAAATAAGATCTACTTT
40033326 TTATAATA
1 TTATAATA
40033334 GTAAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (27 bp):
TTATAATAAAAAAATAAGATCTACTTT
Found at i:40033936 original size:9 final size:9
Alignment explanation
Indices: 40033922--40034038 Score: 107
Period size: 9 Copynumber: 13.0 Consensus size: 9
40033912 CATATCATGT
40033922 CATAACTTA
1 CATAACTTA
40033931 CATAACTTA
1 CATAACTTA
40033940 -ATAACTTA
1 CATAACTTA
* *
40033948 TATATATCATA
1 CATA-A-CTTA
*
40033959 TCATAACTCA
1 -CATAACTTA
40033969 CATAACTTA
1 CATAACTTA
40033978 CATAACTTA
1 CATAACTTA
40033987 CATAACTTA
1 CATAACTTA
40033996 CATAA--TA
1 CATAACTTA
*
40034003 CATAA-ATA
1 CATAACTTA
* * *
40034011 TATATCATA
1 CATAACTTA
40034020 TCATAACTTA
1 -CATAACTTA
40034030 CATAACTTA
1 CATAACTTA
40034039 ATTGTACTTA
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
7 7 0.08
8 13 0.14
9 55 0.60
10 9 0.10
11 4 0.04
12 3 0.03
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:40033952 original size:43 final size:44
Alignment explanation
Indices: 40033905--40034040 Score: 139
Period size: 47 Copynumber: 2.8 Consensus size: 44
40033895 ACTTGACCTG
*
40033905 TATATATCATATCATGTCATAACTTACATAACTTAATAACTT-A
1 TATATATCATATCATATCATAACTTACATAACTTAATAACTTAA
40033948 TATATATCATATCATAACTCACATAACTTACATAACTTACATAACTTACA
1 TATATATCATATCAT-A-T--CATAACTTACATAACTTA-ATAACTTA-A
*
40033998 TAATACATAAATATATATCATATCATAACTTACATAACTTAAT
1 T-AT--AT--AT-CATATCATATCATAACTTACATAACTTAAT
40034041 TGTACTTATA
Statistics
Matches: 78, Mismatches: 2, Indels: 18
0.80 0.02 0.18
Matches are distributed among these distances:
43 15 0.19
45 1 0.01
47 18 0.23
48 7 0.09
50 2 0.03
51 4 0.05
52 18 0.23
53 2 0.03
54 1 0.01
55 3 0.04
56 7 0.09
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.37
Consensus pattern (44 bp):
TATATATCATATCATATCATAACTTACATAACTTAATAACTTAA
Found at i:40033963 original size:38 final size:40
Alignment explanation
Indices: 40033907--40033986 Score: 128
Period size: 38 Copynumber: 2.0 Consensus size: 40
40033897 TTGACCTGTA
* *
40033907 TATATCATATCATGTCATAACTTACATAACTTA-ATAACT
1 TATATCATATCATATCATAACTCACATAACTTACATAACT
40033946 TATAT-ATATCATATCATAACTCACATAACTTACATAACT
1 TATATCATATCATATCATAACTCACATAACTTACATAACT
40033985 TA
1 TA
40033987 CATAACTTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 25 0.66
39 13 0.34
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (40 bp):
TATATCATATCATATCATAACTCACATAACTTACATAACT
Found at i:40034016 original size:56 final size:52
Alignment explanation
Indices: 40033922--40034038 Score: 148
Period size: 56 Copynumber: 2.2 Consensus size: 52
40033912 CATATCATGT
* *
40033922 CATAACTTACATAACTTAATAACTTATATATATCATATCATAACTCACATAACTTA
1 CATAACTTACATAACTTAATAACTCATAAATATCATATCAT-A-T--CATAACTTA
40033978 CATAACTTACATAACTTACATAA-TACATAAATAT-ATATCATATCATAACTTA
1 CATAACTTACATAACTTA-ATAACT-CATAAATATCATATCATATCATAACTTA
40034030 CATAACTTA
1 CATAACTTA
40034039 ATTGTACTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
52 18 0.32
54 1 0.02
55 1 0.02
56 26 0.46
57 11 0.19
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (52 bp):
CATAACTTACATAACTTAATAACTCATAAATATCATATCATATCATAACTTA
Found at i:40035775 original size:12 final size:12
Alignment explanation
Indices: 40035758--40035783 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40035748 AAGATCGAGG
40035758 GATGAATCTGAT
1 GATGAATCTGAT
40035770 GATGAATCTGAT
1 GATGAATCTGAT
40035782 GA
1 GA
40035784 AGAGGATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:40039939 original size:43 final size:43
Alignment explanation
Indices: 40039891--40040082 Score: 158
Period size: 43 Copynumber: 4.5 Consensus size: 43
40039881 GCTCCATTAG
* *
40039891 AGGTCATGTTCTTAAGCGCCATTTGTATGAAAAGAGCCGCTAA
1 AGGTCATGTTCTTTAGCGGCATTTGTATGAAAAGAGCCGCTAA
** **** * * **
40039934 AGGTCACATTCTTTAGCTATGTTTTTAAGAAAAGCA-CTACTAA
1 AGGTCATGTTCTTTAGCGGCATTTGTATGAAAAG-AGCCGCTAA
* * * *
40039977 AGGTCATGTTCTTTAGTGGCGTTTTTGTG-AAAGACGCCGCTAA
1 AGGTCATGTTCTTTAGCGGCATTTGTATGAAAAGA-GCCGCTAA
* *
40040020 AGGTCATGTTCTTTAGTGGCATTTGTGT-AAAA-AGCACTGCTAA
1 AGGTCATGTTCTTTAGCGGCATTTGTATGAAAAGAGC-C-GCTAA
40040063 AGGTCATGTTCTTTAGCGGC
1 AGGTCATGTTCTTTAGCGGC
40040083 GCTTTCTTAA
Statistics
Matches: 119, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
41 3 0.03
42 6 0.05
43 109 0.92
44 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (43 bp):
AGGTCATGTTCTTTAGCGGCATTTGTATGAAAAGAGCCGCTAA
Found at i:40040008 original size:86 final size:84
Alignment explanation
Indices: 40039891--40040083 Score: 212
Period size: 86 Copynumber: 2.2 Consensus size: 84
40039881 GCTCCATTAG
* * *
40039891 AGGTCATGTTCTTAAGCGCCATTTGTATGAAAAGA-GCCGCTAAAGGTCACATTCTTTAGCT-AT
1 AGGTCATGTTCTTTAGCGGCGTTTGTATG-AAAGACGCCGCTAAAGGTCACATTCTTTAG-TGAT
*
40039954 GTT-TTTAAGAAAAGCACTACTAA
64 -TTGTGT-A-AAAAGCACTACTAA
* * * **
40039977 AGGTCATGTTCTTTAGTGGCGTTTTTGTGAAAGACGCCGCTAAAGGTCATGTTCTTTAGTGGCAT
1 AGGTCATGTTCTTTAGCGGCGTTTGTATGAAAGACGCCGCTAAAGGTCACATTCTTTAGT-G-AT
*
40040042 TTGTGTAAAAAGCACTGCTAA
64 TTGTGTAAAAAGCACTACTAA
40040063 AGGTCATGTTCTTTAGCGGCG
1 AGGTCATGTTCTTTAGCGGCG
40040084 CTTTCTTAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
85 6 0.07
86 78 0.86
87 3 0.03
88 4 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (84 bp):
AGGTCATGTTCTTTAGCGGCGTTTGTATGAAAGACGCCGCTAAAGGTCACATTCTTTAGTGATTT
GTGTAAAAAGCACTACTAA
Found at i:40040094 original size:43 final size:42
Alignment explanation
Indices: 40039963--40040119 Score: 167
Period size: 43 Copynumber: 3.7 Consensus size: 42
40039953 TGTTTTTAAG
* *
40039963 AAAAGCACTACTAAAGGTCATGTTCTTTAGTGGCGTTTTTGTGA
1 AAAAGCAC-GCTAAAGGTCATGTTCTTTAGTGGCGTTTCTGT-A
* * *
40040007 AAGACGC-CGCTAAAGGTCATGTTCTTTAGTGGCATTTGTGTA
1 AA-AAGCACGCTAAAGGTCATGTTCTTTAGTGGCGTTTCTGTA
*
40040049 AAAAGCACTGCTAAAGGTCATGTTCTTTAGCGGCGCTTTCT-TA
1 AAAAGCAC-GCTAAAGGTCATGTTCTTTAGTGGCG-TTTCTGTA
* *
40040092 AAAATG-TCGCTAAAAGTCATGTTCTTTA
1 AAAA-GCACGCTAAAGGTCATGTTCTTTA
40040120 ACGGTGTTTT
Statistics
Matches: 98, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
41 3 0.03
42 23 0.23
43 61 0.62
44 8 0.08
45 3 0.03
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (42 bp):
AAAAGCACGCTAAAGGTCATGTTCTTTAGTGGCGTTTCTGTA
Found at i:40054052 original size:89 final size:89
Alignment explanation
Indices: 40053901--40054073 Score: 321
Period size: 89 Copynumber: 1.9 Consensus size: 89
40053891 TTATAAATCA
*
40053901 ATATCATTAAACCGAATTTAACAAATCTCAATCACATGTACATTCATTATACTTATAAATTCATA
1 ATATCATTAAACCAAATTTAACAAATCTCAATCACATGTACATTCATTATACTTATAAATTCATA
40053966 GAACCACATTAAATAACTCGATTT
66 GAACCACATTAAATAACTCGATTT
40053990 ATATCATTAAACCAAATTTAACAAATCTCAATCACATGTACATTCATTATACTTA-AACATTCAT
1 ATATCATTAAACCAAATTTAACAAATCTCAATCACATGTACATTCATTATACTTATAA-ATTCAT
40054054 AGAACCACATTAAATAACTC
65 AGAACCACATTAAATAACTC
40054074 CACTTATCTT
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
88 2 0.02
89 80 0.98
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (89 bp):
ATATCATTAAACCAAATTTAACAAATCTCAATCACATGTACATTCATTATACTTATAAATTCATA
GAACCACATTAAATAACTCGATTT
Found at i:40054767 original size:43 final size:42
Alignment explanation
Indices: 40054720--40054857 Score: 170
Period size: 43 Copynumber: 3.2 Consensus size: 42
40054710 TTGAGTGCTA
*
40054720 ATTAATTAACCAAAGCTATAATTGTATCGCACACTTAGTGCC
1 ATTAATTAACCGAAGCTATAATTGTATCGCACACTTAGTGCC
* * * * *
40054762 GATTAATTAGCTGCAGCTATAATTGTATTGCACTA-TTAGTGCTA
1 -ATTAATTAACCGAAGCTATAATTGTATCGCAC-ACTTAGTGC-C
*
40054806 ATTAATTAGCCGAAGCTATAATTGTATCGCACACTTAGTGCC
1 ATTAATTAACCGAAGCTATAATTGTATCGCACACTTAGTGCC
40054848 ATTATATTAA
1 ATTA-ATTAA
40054858 ACTGAACTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
42 5 0.06
43 74 0.93
44 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (42 bp):
ATTAATTAACCGAAGCTATAATTGTATCGCACACTTAGTGCC
Found at i:40061281 original size:43 final size:43
Alignment explanation
Indices: 40061220--40061356 Score: 193
Period size: 43 Copynumber: 3.2 Consensus size: 43
40061210 GAACTCACAT
* * * *
40061220 ACTTAGTTCTAATTAATTAACCAAAGCTATAATTGTATCGCAC
1 ACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCGCAC
* *
40061263 ACTTAGTGCCAATTAATTAGCTGAAGCTATAATTGTATTGCAC
1 ACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCGCAC
** *
40061306 TGTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCGTAC
1 ACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCGCAC
40061349 ACTTAGTG
1 ACTTAGTG
40061357 TCATTATATT
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 81 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (43 bp):
ACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCGCAC
Found at i:40072824 original size:24 final size:24
Alignment explanation
Indices: 40072796--40072856 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
40072786 AACCGAATTT
* * *
40072796 GCACACATAGTGCTA-ATTACACTC
1 GCACACATAGTGCCATAGTAAAC-C
40072820 GCACACATAGTGCCATAGTAAACC
1 GCACACATAGTGCCATAGTAAACC
40072844 GCACACATAGTGC
1 GCACACATAGTGC
40072857 ATTGGATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (24 bp):
GCACACATAGTGCCATAGTAAACC
Found at i:40077896 original size:31 final size:33
Alignment explanation
Indices: 40077823--40077897 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 33
40077813 AGACTTGTCC
* *
40077823 AAAATAAATCAATAAATTAAAAGACCAAATAAT
1 AAAAGAAATAAATAAATTAAAAGACCAAATAAT
* *
40077856 AAAATAAATAAAT-AATTAAAA-ACCAAATTAT
1 AAAAGAAATAAATAAATTAAAAGACCAAATAAT
*
40077887 CAAAGAAATAA
1 AAAAGAAATAA
40077898 TTTAAAATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 18 0.47
32 8 0.21
33 12 0.32
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.21
Consensus pattern (33 bp):
AAAAGAAATAAATAAATTAAAAGACCAAATAAT
Found at i:40084271 original size:25 final size:25
Alignment explanation
Indices: 40084225--40084275 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
40084215 CCCTTATAAT
* *
40084225 GTGAAAATGACCTTTTTGCCCCTAG
1 GTGAAAATGACCTTTATACCCCTAG
40084250 GTGAAAATGA-CTATTATACCCCTAG
1 GTGAAAATGACCT-TTATACCCCTAG
40084275 G
1 G
40084276 GTTATGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (25 bp):
GTGAAAATGACCTTTATACCCCTAG
Found at i:40084330 original size:10 final size:10
Alignment explanation
Indices: 40084319--40084363 Score: 72
Period size: 10 Copynumber: 4.4 Consensus size: 10
40084309 TTTGTACATA
*
40084319 ATATGCCATA
1 ATATGCCATG
40084329 ATATGCCATG
1 ATATGCCATG
40084339 ATATGCACATG
1 ATATGC-CATG
40084350 ATATGCCATG
1 ATATGCCATG
40084360 ATAT
1 ATAT
40084364 ATATATATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
10 23 0.70
11 10 0.30
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (10 bp):
ATATGCCATG
Found at i:40084355 original size:21 final size:20
Alignment explanation
Indices: 40084319--40084363 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
40084309 TTTGTACATA
40084319 ATATGCCATAATATGCCATG
1 ATATGCCATAATATGCCATG
*
40084339 ATATGCACATGATATGCCATG
1 ATATGC-CATAATATGCCATG
40084360 ATAT
1 ATAT
40084364 ATATATATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (20 bp):
ATATGCCATAATATGCCATG
Found at i:40084436 original size:25 final size:25
Alignment explanation
Indices: 40084408--40084476 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 25
40084398 AGGAAGTGCT
* *
40084408 AAAGGGCTATGCCCTAGTTTACCGA
1 AAAGGGCTATGCCCCAGTTTACCAA
* * *
40084433 AAAGAGCTTTGCCCCAGTTTATCAA
1 AAAGGGCTATGCCCCAGTTTACCAA
* *
40084458 AAAGGGCTTTACCCCAGTT
1 AAAGGGCTATGCCCCAGTT
40084477 ATTAAAAGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (25 bp):
AAAGGGCTATGCCCCAGTTTACCAA
Found at i:40084489 original size:24 final size:25
Alignment explanation
Indices: 40084423--40084489 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
40084413 GCTATGCCCT
* *
40084423 AGTTTACCGAAAAGA-GCTTTGCCCC
1 AGTTTATC-AAAAGAGGCTTTACCCC
40084448 AGTTTATCAAAA-AGGGCTTTACCCC
1 AGTTTATCAAAAGA-GGCTTTACCCC
*
40084473 AG-TTATTAAAAGAGGCT
1 AGTTTATCAAAAGAGGCT
40084490 AGGCCTCCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
23 1 0.03
24 16 0.44
25 19 0.53
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (25 bp):
AGTTTATCAAAAGAGGCTTTACCCC
Found at i:40084735 original size:31 final size:32
Alignment explanation
Indices: 40084697--40084775 Score: 117
Period size: 31 Copynumber: 2.5 Consensus size: 32
40084687 CGTTTACAGT
* *
40084697 AAAGGCTTCGGCCCAGTTGTATGAATAATG-A
1 AAAGGCTTCGGCCCAGTGGTATAAATAATGTA
40084728 AAAGGCTTCGGCCCAGTGGTATAAATAATGTA
1 AAAGGCTTCGGCCCAGTGGTATAAATAATGTA
*
40084760 AAA-GCATCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
40084776 ATATGCTGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 40 0.91
32 4 0.09
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (32 bp):
AAAGGCTTCGGCCCAGTGGTATAAATAATGTA
Found at i:40086129 original size:30 final size:30
Alignment explanation
Indices: 40086093--40086153 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
40086083 TTCCCGAGCC
*
40086093 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
40086123 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
40086153 T
1 T
40086154 GTATTAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:40094508 original size:20 final size:20
Alignment explanation
Indices: 40094483--40094522 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40094473 CTAAAGATCA
40094483 AACGGAGCTCGGTAATTGTC
1 AACGGAGCTCGGTAATTGTC
40094503 AACGGAGCTCGGTAATTGTC
1 AACGGAGCTCGGTAATTGTC
40094523 GAAGGTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (20 bp):
AACGGAGCTCGGTAATTGTC
Found at i:40102698 original size:39 final size:39
Alignment explanation
Indices: 40102655--40102821 Score: 255
Period size: 39 Copynumber: 4.3 Consensus size: 39
40102645 GGTCTTTAAC
** *
40102655 CCGGATATTTTTCCAGCACGTAGCCTGCGAACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGAACCTCATGT
* * *
40102694 CCGGATATATTTCTAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGAACCTCATGT
*
40102733 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGAACCTCATGT
40102772 CCGGATATTTTTCCAGCATATAGCCTGC-AGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGA-ACCTCATGT
40102811 CCGGATATTTT
1 CCGGATATTTT
40102822 CAATCTCATA
Statistics
Matches: 118, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
39 118 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.31
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGAACCTCATGT
Found at i:40105477 original size:46 final size:44
Alignment explanation
Indices: 40105419--40105587 Score: 123
Period size: 46 Copynumber: 3.7 Consensus size: 44
40105409 TCGTAGCCCG
*
40105419 TGCATGTTCCAGACATGTCTTACACTAGCTTATGTTCCAAGGCAGA
1 TGCATGTCCCAGACATGTCTTACACTAGCTTATG-TCCAAGGC-GA
* * *
40105465 TGCATGTCCCAGATACGTCTTACACTAGC--ACTCGTCTCAATGTCGA
1 TGCATGTCCCAGACATGTCTTACACTAGCTTA-T-GTC-CAA-GGCGA
* * *
40105511 TGCCATGTCCCAGACATGGTCTTACACT-G--TCTCTCATAATGTAGCTGA
1 TG-CATGTCCCAGACAT-GTCTTACACTAGCTTATGTC-CAA-G--GC-GA
40105559 TGCATGTCCCAGACATGTCTTACACTAGC
1 TGCATGTCCCAGACATGTCTTACACTAGC
40105588 CCACAATAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
44 1 0.01
45 9 0.09
46 45 0.45
47 31 0.31
48 14 0.14
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (44 bp):
TGCATGTCCCAGACATGTCTTACACTAGCTTATGTCCAAGGCGA
Found at i:40109848 original size:37 final size:37
Alignment explanation
Indices: 40109705--40109850 Score: 247
Period size: 37 Copynumber: 3.9 Consensus size: 37
40109695 AGCTCAGACG
* * * *
40109705 AAATCTCCACATGAAGTTATCGGGTCTTACCCAGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
40109742 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
40109779 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
40109816 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
40109851 ATATATTTCC
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:40110121 original size:47 final size:47
Alignment explanation
Indices: 40110059--40110349 Score: 411
Period size: 47 Copynumber: 6.1 Consensus size: 47
40110049 ACACGTTTCG
* * * **
40110059 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * *
40110106 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
40110153 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
40110200 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* ** *
40110247 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C----ACATACGCATGTTCACATTCATCA
*
40110300 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
40110347 CAT
1 CAT
40110350 AAAATCCTAA
Statistics
Matches: 222, Mismatches: 16, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
47 178 0.80
49 1 0.00
51 1 0.00
53 42 0.19
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:40110331 original size:147 final size:141
Alignment explanation
Indices: 40110059--40110349 Score: 447
Period size: 147 Copynumber: 2.0 Consensus size: 141
40110049 ACACGTTTCG
* **
40110059 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTAGCCATTCGGCCTTACCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* *
40110124 ATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTT
66 ATCTCATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTT
*
40110189 CACATTCATCA
131 CACATCCATCA
* *
40110200 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTAGCCATTCGGCCTTACCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
*
40110265 ATCACGCATATATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACG
66 AT----C-T-CATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACG
40110330 CATGTTCACATCCATCA
125 CATGTTCACATCCATCA
40110347 CAT
1 CAT
40110350 AAAATCCTAA
Statistics
Matches: 135, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
141 62 0.46
145 1 0.01
146 1 0.01
147 71 0.53
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (141 bp):
CATTAGCCATTCGGCCTTACCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCTCATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTT
CACATCCATCA
Found at i:40112420 original size:85 final size:86
Alignment explanation
Indices: 40112291--40112470 Score: 344
Period size: 85 Copynumber: 2.1 Consensus size: 86
40112281 TATTTTATTG
*
40112291 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATG-TTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
40112355 TTAGCCATAACATCTTGTCCA
66 TTAGCCATAACATCTTGTCCA
40112376 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
40112441 TTAGCCATAACATCTTGTCCA
66 TTAGCCATAACATCTTGTCCA
40112462 CCCATGCTC
1 CCCATGCTC
40112471 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 60 0.65
86 33 0.35
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (86 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TTAGCCATAACATCTTGTCCA
Found at i:40118499 original size:21 final size:21
Alignment explanation
Indices: 40118460--40118500 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40118450 AATAATTTGA
** *
40118460 ATAAATTTTATGTATTTTAAT
1 ATAAATTTTATAAAATTTAAT
40118481 ATAAATTTTATAAAATTTAA
1 ATAAATTTTATAAAATTTAA
40118501 AAATTTTCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATAAATTTTATAAAATTTAAT
Found at i:40118566 original size:18 final size:18
Alignment explanation
Indices: 40118539--40118573 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40118529 AATATTTTTA
40118539 TAATTCTTTATAAATTTC
1 TAATTCTTTATAAATTTC
* *
40118557 TAATTTTTTATGAATTT
1 TAATTCTTTATAAATTT
40118574 TATAATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (18 bp):
TAATTCTTTATAAATTTC
Found at i:40121818 original size:28 final size:28
Alignment explanation
Indices: 40121787--40121849 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
40121777 CATCTGATAG
40121787 TTAACTTGCAATAAAGTGAGATCTTTTT
1 TTAACTTGCAATAAAGTGAGATCTTTTT
*
40121815 TTAACTTGTAATAAAGTGAGATCTTTTT
1 TTAACTTGCAATAAAGTGAGATCTTTTT
*
40121843 TGAACTT
1 TTAACTT
40121850 TTGGTTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (28 bp):
TTAACTTGCAATAAAGTGAGATCTTTTT
Found at i:40122231 original size:98 final size:98
Alignment explanation
Indices: 40122062--40122254 Score: 323
Period size: 98 Copynumber: 2.0 Consensus size: 98
40122052 CAACTTTATT
* * * *
40122062 TAAGGATTCACTCATTTTTTTGCGTTGTGGTGGAGCAATTGGAACATATACACATATGCAAAAAT
1 TAAGGATTCACTCATCTTTGTGCGTTATGATGGAGCAATTGGAACATATACACATATGCAAAAAT
*
40122127 TTACTGTCAATGTTACACGGTCTAGGCTATTTA
66 TTACTGTCAATGTTACACAGTCTAGGCTATTTA
40122160 TAAGGATTCACTCATCTTTGTGCGTTATGATGGAGCAATTGGAACATATACACATATGCAAAAAT
1 TAAGGATTCACTCATCTTTGTGCGTTATGATGGAGCAATTGGAACATATACACATATGCAAAAAT
* *
40122225 TTACTGTCGATGTTACACAGTGTAGGCTAT
66 TTACTGTCAATGTTACACAGTCTAGGCTAT
40122255 GTAGGCTGTG
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (98 bp):
TAAGGATTCACTCATCTTTGTGCGTTATGATGGAGCAATTGGAACATATACACATATGCAAAAAT
TTACTGTCAATGTTACACAGTCTAGGCTATTTA
Found at i:40125600 original size:14 final size:14
Alignment explanation
Indices: 40125583--40125612 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40125573 AATGAAACAT
40125583 ATGGTTTGAAATAA
1 ATGGTTTGAAATAA
40125597 ATGGTTTGAAATAA
1 ATGGTTTGAAATAA
40125611 AT
1 AT
40125613 TAATAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (14 bp):
ATGGTTTGAAATAA
Found at i:40127321 original size:27 final size:27
Alignment explanation
Indices: 40127283--40127339 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
40127273 TCATTGCTAG
40127283 TATGTTCATTGTGAATCTTGTGTTTGA
1 TATGTTCATTGTGAATCTTGTGTTTGA
40127310 TATGTTCATTGTGAATCTTGTGTTTGA
1 TATGTTCATTGTGAATCTTGTGTTTGA
40127337 TAT
1 TAT
40127340 ATTACATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.07, G:0.21, T:0.53
Consensus pattern (27 bp):
TATGTTCATTGTGAATCTTGTGTTTGA
Found at i:40129238 original size:15 final size:16
Alignment explanation
Indices: 40129218--40129248 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
40129208 CTCACTTTTC
40129218 TTTATTTAA-TAATTA
1 TTTATTTAATTAATTA
40129233 TTTATTTAATTAATTA
1 TTTATTTAATTAATTA
40129249 AATCAATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATTTAATTAATTA
Found at i:40133257 original size:14 final size:14
Alignment explanation
Indices: 40133238--40133266 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40133228 ACTATAACAA
40133238 TAGTCACTAACCTT
1 TAGTCACTAACCTT
40133252 TAGTCACTAACCTT
1 TAGTCACTAACCTT
40133266 T
1 T
40133267 GGTAAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.38
Consensus pattern (14 bp):
TAGTCACTAACCTT
Found at i:40134149 original size:85 final size:85
Alignment explanation
Indices: 40134006--40134184 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
40133996 GGCCGGCCAT
40134006 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
40134071 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
40134091 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
40134156 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
40134176 GGGCATGGG
1 GAGCATGGG
40134185 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:40135497 original size:47 final size:47
Alignment explanation
Indices: 40135446--40135885 Score: 547
Period size: 47 Copynumber: 9.1 Consensus size: 47
40135436 TTAGGATTTT
* * *
40135446 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGTCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
**
40135493 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCATATGTGTGATAAGGCCGAATGGCCA
*
40135544 ATGTGATGAATGTGAACATGCATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
**
40135591 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCATATGTGTGATAAGGCCGAATGGCCA
** * **
40135642 ATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCTT
1 ATGTGATGAATGTGAA-C-----ATGCATATGTGTGATAAGGCCGAATGGCCA
*
40135695 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
40135742 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGACCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
** *
40135789 ATGTGATGAATGTGAACATGCATAAATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* * * *
40135836 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
40135883 ATG
1 ATG
40135886 CGAAACGTGT
Statistics
Matches: 350, Mismatches: 32, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
47 215 0.61
49 3 0.01
50 2 0.01
51 85 0.24
52 1 0.00
53 44 0.13
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:40135550 original size:22 final size:22
Alignment explanation
Indices: 40135523--40135597 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
40135513 TATATATATG
40135523 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* *
40135545 TGTGATGAATG-TGAACAT-G-CATA
1 TGTGAT-AAGGCCG-A-ATGGCCA-A
40135568 TGCGTGATAAGGCCGAATGGCCAA
1 T--GTGATAAGGCCGAATGGCCAA
40135592 TGTGAT
1 TGTGAT
40135598 GAATGTGAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 14 0.35
23 9 0.22
24 9 0.22
25 8 0.20
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.24
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:40135557 original size:98 final size:98
Alignment explanation
Indices: 40135446--40135885 Score: 572
Period size: 98 Copynumber: 4.5 Consensus size: 98
40135436 TTAGGATTTT
* * *
40135446 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGTCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
40135511 CGTATATATATGTGTGATAAGGCCGAATGGCCA
66 CGTATATATATGTGTGATAAGGCCGAATGGCCA
*
40135544 ATGTGATGAATGTGAACATGCATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
40135609 CGTATATATATGTGTGATAAGGCCGAATGGCCA
66 CGTATATATATGTGTGATAAGGCCGAATGGCCA
** * **
40135642 ATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCTTATGTGATGAATG
1 ATGTGATGAATGTGAA-C-----ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATG
***
40135707 TGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
60 TGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
* * *
40135742 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGACCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
* * *
40135807 TGCATA-A-A--TGAGATAAGGCCGAATGGCCA
66 CGTATATATATGTGTGATAAGGCCGAATGGCCA
* * * *
40135836 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTAATG
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATG
40135886 CGAAACGTGT
Statistics
Matches: 304, Mismatches: 28, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
94 103 0.34
96 1 0.00
98 112 0.37
99 2 0.01
100 43 0.14
102 1 0.00
104 42 0.14
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (98 bp):
ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
CGTATATATATGTGTGATAAGGCCGAATGGCCA
Found at i:40135721 original size:23 final size:23
Alignment explanation
Indices: 40135694--40135769 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
40135684 CCGAATGGCT
40135694 TATGTGATGAATGTGAACATGCG
1 TATGTGATGAATGTGAACATGCG
* * *
40135717 TATGTG-TGATAAG-G-CCGAATGGCC
1 TATGTGATGA-ATGTGAAC--AT-GCG
*
40135741 AATGTGATGAATGTGAACATGCG
1 TATGTGATGAATGTGAACATGCG
40135764 TATGTG
1 TATGTG
40135770 TGATAAGGCC
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
21 1 0.03
22 4 0.11
23 17 0.45
24 11 0.29
25 4 0.11
26 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.29
Consensus pattern (23 bp):
TATGTGATGAATGTGAACATGCG
Found at i:40135726 original size:25 final size:25
Alignment explanation
Indices: 40135696--40135773 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
40135686 GAATGGCTTA
40135696 TGTGATGAATGTGAACATGCGTATG
1 TGTGATGAATGTGAACATGCGTATG
* * * *
40135721 TGTGAT-AAGGCCG-A-ATG-GCCA-A
1 TGTGATGAATG-TGAACATGCG-TATG
40135743 TGTGATGAATGTGAACATGCGTATG
1 TGTGATGAATGTGAACATGCGTATG
40135768 TGTGAT
1 TGTGAT
40135774 AAGGCCGAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
22 8 0.21
23 8 0.21
24 8 0.21
25 14 0.37
ACGTcount: A:0.28, C:0.10, G:0.32, T:0.29
Consensus pattern (25 bp):
TGTGATGAATGTGAACATGCGTATG
Found at i:40135948 original size:46 final size:46
Alignment explanation
Indices: 40135859--40135949 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
40135849 GAACATGAAT
* * * *
40135859 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
* * *
40135905 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTACGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATG
40135950 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.32, T:0.25
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
Found at i:40136144 original size:37 final size:37
Alignment explanation
Indices: 40136094--40136239 Score: 247
Period size: 37 Copynumber: 3.9 Consensus size: 37
40136084 GGAAATATAT
*
40136094 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
40136131 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
40136168 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * * *
40136205 TCCGGGTAAGACCCAATAACTTCATGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
40136240 CGTCTGAGCT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:40137195 original size:16 final size:16
Alignment explanation
Indices: 40137167--40137200 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
40137157 AGCAATTTAA
40137167 TTTTTTTCTTTTAACTT
1 TTTTTTTCTTTTAA-TT
40137184 TTTTTTTC-TTTAATT
1 TTTTTTTCTTTTAATT
40137199 TT
1 TT
40137201 CATTCTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 5 0.29
17 8 0.47
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTCTTTTAATT
Found at i:40139197 original size:21 final size:18
Alignment explanation
Indices: 40139180--40139226 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
40139170 TTCATGGCCT
40139180 TGGTCAAAATTATAATGG
1 TGGTCAAAATTATAATGG
*
40139198 TAGTCAAAATTATAATGG
1 TGGTCAAAATTATAATGG
40139216 TGGTCAAAATT
1 TGGTCAAAATT
40139227 GCTCTCTGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.34
Consensus pattern (18 bp):
TGGTCAAAATTATAATGG
Found at i:40147796 original size:17 final size:17
Alignment explanation
Indices: 40147774--40147808 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
40147764 ATTGAGAGTT
40147774 CTTATGAAGCAATTTAA
1 CTTATGAAGCAATTTAA
40147791 CTTATGAAGCAATTTAA
1 CTTATGAAGCAATTTAA
40147808 C
1 C
40147809 CAGATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (17 bp):
CTTATGAAGCAATTTAA
Found at i:40156179 original size:27 final size:27
Alignment explanation
Indices: 40156149--40156407 Score: 270
Period size: 27 Copynumber: 9.6 Consensus size: 27
40156139 ATATTGAGTC
* * * *
40156149 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAATT
* * *
40156176 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAATT
* *
40156203 CGCACACTTAGTGCTTCATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AATT
** *
40156231 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAATT
* *
40156258 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAATT
* *
40156285 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAATT
** *
40156312 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAATT
* *
40156339 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAATT
* *
40156366 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAATT
40156393 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40156408 GTACAATTTA
Statistics
Matches: 196, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
27 171 0.87
28 25 0.13
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAATT
Found at i:40156350 original size:81 final size:81
Alignment explanation
Indices: 40156170--40156406 Score: 386
Period size: 81 Copynumber: 2.9 Consensus size: 81
40156160 TGCTATATAA
* * * ** **
40156170 TCAACTCGCACACTTAGTGC-TACGTAATCAAATCGCACACTTAGTGCTTCATAGTCAAACTCGC
1 TCAATTCGCACACTTAGTGCAT-CATATTCATTTCGCACACTTAGTGCAACATAGTCAAA-TCGC
40156234 ACACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
40156252 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
40156317 ACTTAGTGCCGCATGG
66 ACTTAGTGCCGCATGG
40156333 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
40156398 ACTTAGTGC
66 ACTTAGTGC
40156407 TGTACAATTT
Statistics
Matches: 147, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
81 96 0.65
82 50 0.34
83 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (81 bp):
TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40172032 original size:48 final size:48
Alignment explanation
Indices: 40171961--40172080 Score: 231
Period size: 48 Copynumber: 2.5 Consensus size: 48
40171951 ATTACAAACA
40171961 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
*
40172009 TCAATTATTTACCCTATTAACAAATAATCTCCTTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
40172057 TCAATTATTTACCCTATTAACAAA
1 TCAATTATTTACCCTATTAACAAA
40172081 GCTCGGACTA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (48 bp):
TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
Found at i:40177730 original size:20 final size:21
Alignment explanation
Indices: 40177697--40177735 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40177687 AACTCAATGG
40177697 AGCTCAATTCAGCTCAATTCT
1 AGCTCAATTCAGCTCAATTCT
*
40177718 AGCTC-ATTGAGCTCAATT
1 AGCTCAATTCAGCTCAATT
40177736 TTATCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (21 bp):
AGCTCAATTCAGCTCAATTCT
Done.