Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 123 of 203
Found at i:39078477 original size:33 final size:34
Alignment explanation
Indices: 39078384--39078482 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 34
39078374 TAAGGCTCAC
* *
39078384 ACTGTTACTGCATCGGGCTAAGGCCCACACTGTT
1 ACTGTTACTGAATAGGGCTAAGGCCCACACTGTT
*
39078418 ACTG---C---ATCGGGCTAAGGCCCACACTG-T
1 ACTGTTACTGAATAGGGCTAAGGCCCACACTGTT
** * *
39078445 ACTGTTACTGAATAGGGCTCGGGCCTAGACTGTT
1 ACTGTTACTGAATAGGGCTAAGGCCCACACTGTT
39078479 ACTG
1 ACTG
39078483 CATGTTGTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
27 5 0.09
28 21 0.40
30 1 0.02
31 1 0.02
33 16 0.30
34 9 0.17
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.25
Consensus pattern (34 bp):
ACTGTTACTGAATAGGGCTAAGGCCCACACTGTT
Found at i:39079204 original size:9 final size:9
Alignment explanation
Indices: 39079190--39079301 Score: 147
Period size: 9 Copynumber: 12.4 Consensus size: 9
39079180 TTTGGTTAAA
39079190 AATTAACCG
1 AATTAACCG
39079199 AATTAACCG
1 AATTAACCG
*
39079208 AATTACCCG
1 AATTAACCG
39079217 AATTAACCG
1 AATTAACCG
39079226 AATT-ACCTG
1 AATTAACC-G
*
39079235 AATTAACTG
1 AATTAACCG
39079244 AATTAACCG
1 AATTAACCG
*
39079253 GATT-ACCGG
1 AATTAACC-G
39079262 AATTAACCG
1 AATTAACCG
*
39079271 AATTACCCG
1 AATTAACCG
*
39079280 AATTAATCG
1 AATTAACCG
39079289 AATTAACCG
1 AATTAACCG
39079298 AATT
1 AATT
39079302 GAATCACTAC
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
8 6 0.07
9 78 0.88
10 5 0.06
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:39079375 original size:20 final size:20
Alignment explanation
Indices: 39079346--39079389 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39079336 TAGACTTTAG
39079346 TTTTAGTTTTAGTT-TTAGAA
1 TTTTAGTTTTAGTTATTA-AA
* *
39079366 TTTTATTTTTATTTATTAAA
1 TTTTAGTTTTAGTTATTAAA
39079386 TTTT
1 TTTT
39079390 TGTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTTAGTTTTAGTTATTAAA
Found at i:39079443 original size:18 final size:18
Alignment explanation
Indices: 39079403--39079446 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39079393 AATTTTTATG
**
39079403 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
39079421 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
39079439 CTTGGGTT
1 ATTGGGTT
39079447 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:39080041 original size:75 final size:75
Alignment explanation
Indices: 39079905--39080052 Score: 219
Period size: 75 Copynumber: 2.0 Consensus size: 75
39079895 GGAAAACCAA
* *
39079905 GATTATTCCCTTATTAATAGAGAATGAAAATGGAAAGTTAGAAAAAGCTATTACATTCTTTCCAA
1 GATTATTCCCTTATTAATAGAGAATGAAAATGGAAAGTTAGAAAAAGCAATTACATGCTTTCCAA
*
39079970 AAGAATATAG
66 AAAAATATAG
* *
39079980 GATTATTCCCTTATTAATAGAGAA-GACAAATGGAAATTTAGAAAAATG-AATTATATGCTTTCC
1 GATTATTCCCTTATTAATAGAGAATGA-AAATGGAAAGTTAGAAAAA-GCAATTACATGCTTTCC
39080043 AAAAAAATAT
64 AAAAAAATAT
39080053 TAATTTCCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
74 2 0.03
75 63 0.95
76 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (75 bp):
GATTATTCCCTTATTAATAGAGAATGAAAATGGAAAGTTAGAAAAAGCAATTACATGCTTTCCAA
AAAAATATAG
Found at i:39091547 original size:683 final size:682
Alignment explanation
Indices: 39090243--39091607 Score: 2089
Period size: 683 Copynumber: 2.0 Consensus size: 682
39090233 TAACAACTGA
*
39090243 GCAAGAAGAGAAACTCATCCTAGTGTTGAAACAATTCAAAAAGGGTATCAGATGGACCATAGCCG
1 GCAAGAAGAGAAACTCATCCTAGTGTTGAAACAATTCAAAAAGGCTATCAGATGGACCATAGCCG
* * *
39090308 ATATTCGCAGAATTAGTCCATCTGTATGCATGCACAAGATTATCTTAGAAAATGACGAAAAGGGT
66 ATATTCACAAAATTAGTCCATCTGTATGCATGCACAAGATTATCTTAGAAAATGACGAAAAGAGT
* * *
39090373 ACGATTAATGGACAACGAAGAATGAACCCTATCTTGAAGGACGTAGTCAAGAAAGAAATCATCAA
131 ACGATTAATGGACAACGAAAAATGAACCCCATCATGAAGGACGTAGTCAAGAAAGAAATCATCAA
* *
39090438 GTGTTAGATGGGGGTATAATTTACCCCATCTCAGATAGTTCATACGTAAGTCTGATCCAGTGCGT
196 GTGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATACGTAAGTCAGATCCAGTGCGT
* * * *
39090503 GCCAAAGAAAAGAGGTATCACGGTCATTAAGAAGAAGAATAATGAGTTGATACCGACTAGAACGG
261 GCCAAAGAAAAGAGGTATCACGGCCATTAAGAAGAAGAATAACGAGTTGATACCAAATAGAACGG
*
39090568 TGACGGGATGGAGAATTTGCATCAATTACCAGAAGTTGAACAAGGCAACCAGGAAAGATCACTTT
326 TGACGGGATGGAGAATTTGCATCAATTACCAGAAGCTGAACAAGGCAACCAGGAAAGATCACTTT
* *
39090633 CCTTTGTCGTTTTTGGACCAGATGCTAGATAGACTCGCAGGGCGAGACTATTACTATTTTCTCGA
391 CCTTTGCCGTTTTTAGACCAGATGCTAGATAGACTCGCAGGGCGAGACTATTACTATTTTCTCGA
* * * ** * * *
39090698 TGGATACTTGGGGTATATTCAGATTACAGTAGCATTGAAAGATCAGCACAAGACAACATTCACCT
456 TGGATACTCGGGGTATAATCAAATTACAGTAGCACAGAAAGATCAACAAAAGAAAACATTCACCT
* * *
39090763 GCTCGTATGGTACGCTTTCATTTAGGCGCATGCCATTTGGTTTATGCAATGCACCTGCTACATTT
521 GCTCGTACGGTACGCTTACATTTAGGCACATGCCATTTGGTTTATGCAATGCACCTGCTACATTT
* *
39090828 CAAATAACTATGATGTCTATTTTTACTGACATGGTTGAGAAATATTTGGAAGTTTTTATGGATGA
586 CAAATAACTATAATGTCTATTTTTACTGACATGGTTGAGAAATATTTGAAAGTTTTTATGGATGA
39090893 TTTTTCAGTATTCAGAGATACATATGATGATT
651 TTTTTCAGTATTCAGAGATACATATGATGATT
* * * *
39090925 GCAAGAAGAGAAACTCATCCTGGTGTTGAAACAATTCAAGAAGGCTATCGGATGGACCATAGCTG
1 GCAAGAAGAGAAACTCATCCTAGTGTTGAAACAATTCAAAAAGGCTATCAGATGGACCATAGCCG
* *
39090990 ATATTCACAAAATTAGTCCATCTGTATGCATGCATAAGATTATCTTAGAAAATGGCGAAAAAGAG
66 ATATTCACAAAATTAGTCCATCTGTATGCATGCACAAGATTATCTTAGAAAATGACG-AAAAGAG
* * *
39091055 -ACGATTGATGGTCAAC-AAAAACTGAACCCCATCATGAAGGACGTAGTTAAGAAAGAAATCATC
130 TACGATTAATGGACAACGAAAAA-TGAACCCCATCATGAAGGACGTAGTCAAGAAAGAAATCATC
**
39091118 AAGTGGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATGGGTAAGTCCAG-TCCAGT
194 AAGT-GTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATACGTAAGT-CAGATCCAGT
39091182 GCGTGCCAAAGAAAAGAGGTATCACGGCCATTGAA-AATG-AGAATAACGAGTTGATACCAAATA
257 GCGTGCCAAAGAAAAGAGGTATCACGGCCATT-AAGAA-GAAGAATAACGAGTTGATACCAAATA
* * * * *
39091245 GAACGGTTACGGGATGGAGAATTTGCATCGATTATC-GAAAGCTGAACTAGGCAACTAGGAAAGA
320 GAACGGTGACGGGATGGAGAATTTGCATCAATTACCAG-AAGCTGAACAAGGCAACCAGGAAAGA
* * *
39091309 TCACTTTCCTTTGCCGTTTTTAGACCAGATGCTGGATAGACTCGTAGGGTGAGACTATTACTATT
384 TCACTTTCCTTTGCCGTTTTTAGACCAGATGCTAGATAGACTCGCAGGGCGAGACTATTACTATT
39091374 TTCTCGATGGATACTCGGGGTATAATCAAATTACAGTAGCACCAG-AAGATCAACAAAAGAAAAC
449 TTCTCGATGGATACTCGGGGTATAATCAAATTACAGTAGCA-CAGAAAGATCAACAAAAGAAAAC
* * *
39091438 ATTCACCTTCTCGTACGGTAC-ATCTACATTTAGGCACATGCCATTTGGTTTATGTAATGCACCT
513 ATTCACCTGCTCGTACGGTACGCT-TACATTTAGGCACATGCCATTTGGTTTATGCAATGCACCT
** *
39091502 GCTACATTTCAAATATGTCTAATGTCTATTTTTACTGACATGGTTGAGAAATATTTGAAAGTTTT
577 GCTACATTTCAAATAACTATAATGTCTATTTTTACTGACATGGTTGAGAAATATTTGAAAGTTTT
* *
39091567 TATGGATGATTTTTTAGTATTCGGAGATACATATGATGATT
642 TATGGATGATTTTTCAGTATTCAGAGATACATATGATGATT
39091608 TCCTAAACAA
Statistics
Matches: 618, Mismatches: 56, Indels: 17
0.89 0.08 0.02
Matches are distributed among these distances:
681 4 0.01
682 171 0.28
683 437 0.71
684 6 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (682 bp):
GCAAGAAGAGAAACTCATCCTAGTGTTGAAACAATTCAAAAAGGCTATCAGATGGACCATAGCCG
ATATTCACAAAATTAGTCCATCTGTATGCATGCACAAGATTATCTTAGAAAATGACGAAAAGAGT
ACGATTAATGGACAACGAAAAATGAACCCCATCATGAAGGACGTAGTCAAGAAAGAAATCATCAA
GTGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATACGTAAGTCAGATCCAGTGCGT
GCCAAAGAAAAGAGGTATCACGGCCATTAAGAAGAAGAATAACGAGTTGATACCAAATAGAACGG
TGACGGGATGGAGAATTTGCATCAATTACCAGAAGCTGAACAAGGCAACCAGGAAAGATCACTTT
CCTTTGCCGTTTTTAGACCAGATGCTAGATAGACTCGCAGGGCGAGACTATTACTATTTTCTCGA
TGGATACTCGGGGTATAATCAAATTACAGTAGCACAGAAAGATCAACAAAAGAAAACATTCACCT
GCTCGTACGGTACGCTTACATTTAGGCACATGCCATTTGGTTTATGCAATGCACCTGCTACATTT
CAAATAACTATAATGTCTATTTTTACTGACATGGTTGAGAAATATTTGAAAGTTTTTATGGATGA
TTTTTCAGTATTCAGAGATACATATGATGATT
Found at i:39096650 original size:104 final size:104
Alignment explanation
Indices: 39096528--39096730 Score: 397
Period size: 104 Copynumber: 2.0 Consensus size: 104
39096518 GTAATTATTT
39096528 TTAATTTGTGCATTACTCGAGATGAGCAATGAATTAAGTTTGGGGTGTGGAAACACGAAAATTTA
1 TTAATTTGTGCATTACTCGAGATGAGCAATGAATTAAGTTTGGGGTGTGGAAACACGAAAATTTA
*
39096593 CACATTTTTACATACCCTTTTTAACTTAAAATCACACAG
66 CACATTTTTACATACCCTTTTAAACTTAAAATCACACAG
39096632 TTAATTTGTGCATTACTCGAGATGAGCAATGAATTAAGTTTGGGGTGTGGAAACACGAAAATTTA
1 TTAATTTGTGCATTACTCGAGATGAGCAATGAATTAAGTTTGGGGTGTGGAAACACGAAAATTTA
39096697 CACATTTTTACATACCCTTTTAAACTTAAAATCA
66 CACATTTTTACATACCCTTTTAAACTTAAAATCA
39096731 TACAATTTTG
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 98 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (104 bp):
TTAATTTGTGCATTACTCGAGATGAGCAATGAATTAAGTTTGGGGTGTGGAAACACGAAAATTTA
CACATTTTTACATACCCTTTTAAACTTAAAATCACACAG
Found at i:39097734 original size:21 final size:20
Alignment explanation
Indices: 39097689--39097734 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
39097679 TTGTCCGAAT
39097689 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
39097708 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
39097729 GGTTGA
1 GGTTGA
39097735 TTGCATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:39099272 original size:19 final size:19
Alignment explanation
Indices: 39099231--39099272 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
39099221 ATTGAACTTG
* *
39099231 AAAATTGGACTAGAGATCG
1 AAAATTGGACTAGAGAACC
39099250 AAAATTGGAACTA-AGAACC
1 AAAATTGG-ACTAGAGAACC
39099269 AAAA
1 AAAA
39099273 ACTGAGATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17
Consensus pattern (19 bp):
AAAATTGGACTAGAGAACC
Found at i:39099632 original size:17 final size:17
Alignment explanation
Indices: 39099612--39099709 Score: 62
Period size: 17 Copynumber: 5.8 Consensus size: 17
39099602 TATTTTTATA
39099612 AATTTAATATTTAATTT
1 AATTTAATATTTAATTT
*
39099629 AATTTAATACTT-ATCTT
1 AATTTAATATTTAAT-TT
* *
39099646 GA--TAATATTTTA-TT
1 AATTTAATATTTAATTT
*
39099660 AATTTAATATTAAAGTGATT
1 AATTTAATATTTAA-T--TT
*
39099680 -ATCTTAATATTAAATTT
1 AAT-TTAATATTTAATTT
*
39099697 AATCTAATATTTA
1 AATTTAATATTTA
39099710 TATTGATAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 3 0.05
15 7 0.11
16 11 0.17
17 24 0.38
18 2 0.03
19 3 0.05
20 13 0.21
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTAATATTTAATTT
Found at i:39099705 original size:68 final size:69
Alignment explanation
Indices: 39099615--39099744 Score: 208
Period size: 68 Copynumber: 1.9 Consensus size: 69
39099605 TTTTATAAAT
* * * *
39099615 TTAATATTTAATTTAATTTAATACTTATCTTGATAAT-ATTTTATTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATCTAATACTTATATTGATAATCATTATATTAATTTAATATTAAAGTGAT
39099679 TATC
66 TATC
*
39099683 TTAATATTAAATTTAATCTAATATTTATATTGATAATCATTATATTAATTTAATATTAAAGT
1 TTAATATTAAATTTAATCTAATACTTATATTGATAATCATTATATTAATTTAATATTAAAGT
39099745 TCTTAAGGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
68 33 0.59
69 23 0.41
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (69 bp):
TTAATATTAAATTTAATCTAATACTTATATTGATAATCATTATATTAATTTAATATTAAAGTGAT
TATC
Found at i:39100649 original size:13 final size:13
Alignment explanation
Indices: 39100628--39100676 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
39100618 TTTAGTTTGG
39100628 ATTTTTATTTT-T
1 ATTTTTATTTTCT
39100640 ATTTTCTA-TTTCT
1 ATTTT-TATTTTCT
39100653 ATTTTT-TTCTTCT
1 ATTTTTATT-TTCT
*
39100666 ATTTTTGTTTT
1 ATTTTTATTTT
39100677 GGTTTGCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 10 0.31
13 20 0.62
14 2 0.06
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (13 bp):
ATTTTTATTTTCT
Found at i:39100650 original size:19 final size:19
Alignment explanation
Indices: 39100628--39100676 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
39100618 TTTAGTTTGG
39100628 ATTTTTATTTTTATT-TTCT
1 ATTTTTATTTTT-TTCTTCT
*
39100647 ATTTCTATTTTTTTCTTCT
1 ATTTTTATTTTTTTCTTCT
*
39100666 ATTTTTGTTTT
1 ATTTTTATTTT
39100677 GGTTTGCACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (19 bp):
ATTTTTATTTTTTTCTTCT
Found at i:39103254 original size:72 final size:72
Alignment explanation
Indices: 39103143--39103286 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
39103133 TATTCAAAGG
* *
39103143 ATTCACAATGACCAGCTAATTTAATTTCATTTTCGAACTTCAATTGTTTACTTAAATAATAATTC
1 ATTCACAATGACCAGCTAATTTAATTACATTTTCAAACTTCAATTGTTTACTTAAATAATAATTC
39103208 GAAAAAC
66 GAAAAAC
* *
39103215 ATTCACAATGACCAGTTAATTTAATTACATTTTCAAACTTCAATTTTTTACTTAAATAATAATTC
1 ATTCACAATGACCAGCTAATTTAATTACATTTTCAAACTTCAATTGTTTACTTAAATAATAATTC
39103280 GAAAAAC
66 GAAAAAC
39103287 TTAACTTAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (72 bp):
ATTCACAATGACCAGCTAATTTAATTACATTTTCAAACTTCAATTGTTTACTTAAATAATAATTC
GAAAAAC
Found at i:39105515 original size:50 final size:50
Alignment explanation
Indices: 39105405--39105604 Score: 179
Period size: 50 Copynumber: 3.9 Consensus size: 50
39105395 ACATTTGGGT
* * *
39105405 GATGAGA--TCCCATATAAGACCATGTTTGGGACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA
* *
39105456 GATTATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
*** * *
39105509 GATGAGAGGTCCCCCATAAAACCATGTCTGGGACATGGCATGGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * ** * * *
39105559 TATGCGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39105605 GTACAAGAAA
Statistics
Matches: 120, Mismatches: 24, Indels: 11
0.77 0.15 0.07
Matches are distributed among these distances:
50 76 0.63
51 1 0.01
53 3 0.03
54 6 0.05
55 1 0.01
56 33 0.28
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:39109107 original size:14 final size:14
Alignment explanation
Indices: 39109088--39109117 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39109078 ATCATCATTA
39109088 TTTTCTCTTTCAGG
1 TTTTCTCTTTCAGG
39109102 TTTTCTCTTTCAGG
1 TTTTCTCTTTCAGG
39109116 TT
1 TT
39109118 ATAAAACAAA
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:0.07, C:0.20, G:0.13, T:0.60
Consensus pattern (14 bp):
TTTTCTCTTTCAGG
Found at i:39113776 original size:18 final size:18
Alignment explanation
Indices: 39113730--39113780 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
39113720 AGCTCTCAGG
39113730 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* * ***
39113748 TAGTAAGCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
39113766 CATTCTTCTCCCTTC
1 CATTCTTCTCCCTTC
39113781 CTTCATTCCT
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.41, G:0.04, T:0.41
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:39116114 original size:14 final size:14
Alignment explanation
Indices: 39116095--39116124 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39116085 TAGTTGAGGG
39116095 ATGACGATTCTCCT
1 ATGACGATTCTCCT
39116109 ATGACGATTCTCCT
1 ATGACGATTCTCCT
39116123 AT
1 AT
39116125 CTTCTAGACA
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:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (14 bp):
ATGACGATTCTCCT
Found at i:39116861 original size:14 final size:15
Alignment explanation
Indices: 39116830--39116868 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
39116820 AAACACTAAA
39116830 AAAT-ATTTTCCAGT
1 AAATCATTTTCCAGT
39116844 AAATCATTTTCCAG-
1 AAATCATTTTCCAGT
39116858 AAATCATTTTC
1 AAATCATTTTC
39116869 TGAAAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (15 bp):
AAATCATTTTCCAGT
Found at i:39130226 original size:9 final size:9
Alignment explanation
Indices: 39130212--39130238 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
39130202 CTATTTCATG
39130212 TTAATTAAT
1 TTAATTAAT
39130221 TTAATTAAT
1 TTAATTAAT
39130230 TTAATTAAT
1 TTAATTAAT
39130239 ATTTTAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAATTAAT
Found at i:39131479 original size:28 final size:28
Alignment explanation
Indices: 39131439--39131493 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
39131429 ATAAGTGGGA
39131439 GATCCAACACTTAATGCATGTTATATTT
1 GATCCAACACTTAATGCATGTTATATTT
* **
39131467 GATCCAACGCTTAATGTGTGTTATATT
1 GATCCAACACTTAATGCATGTTATATT
39131494 GCAATAGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (28 bp):
GATCCAACACTTAATGCATGTTATATTT
Found at i:39132393 original size:21 final size:21
Alignment explanation
Indices: 39132355--39132394 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39132345 TAATAATGTC
*
39132355 TCAAAACATTAAGAACATACA
1 TCAAAACATCAAGAACATACA
* *
39132376 TCAAAACCTCAAGTACATA
1 TCAAAACATCAAGAACATA
39132395 ATTAATTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.23, G:0.05, T:0.20
Consensus pattern (21 bp):
TCAAAACATCAAGAACATACA
Found at i:39132473 original size:68 final size:68
Alignment explanation
Indices: 39132383--39132530 Score: 248
Period size: 68 Copynumber: 2.2 Consensus size: 68
39132373 ACATCAAAAC
* *
39132383 CTCAAG-T-ACATAATTAATTATTTGGAGCATATCGCAAATTTTGGTCTTGAGAGTAAACAAACA
1 CTCAAGATAACATGATTAATTATTTGGAGCATATCGCAAATTTTGGTCTTGAGACTAAACAAACA
39132446 AAT
66 AAT
*
39132449 CTCAAGATAACATGATTAATTATTTGGTGCATATCGCAAATTTTGGTCTTGAGACTAAACAAACA
1 CTCAAGATAACATGATTAATTATTTGGAGCATATCGCAAATTTTGGTCTTGAGACTAAACAAACA
39132514 AAT
66 AAT
39132517 CTC-AGATAACATGA
1 CTCAAGATAACATGA
39132531 CTCAAATCTC
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
66 6 0.08
67 12 0.16
68 59 0.77
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (68 bp):
CTCAAGATAACATGATTAATTATTTGGAGCATATCGCAAATTTTGGTCTTGAGACTAAACAAACA
AAT
Found at i:39137931 original size:52 final size:52
Alignment explanation
Indices: 39137853--39137999 Score: 285
Period size: 52 Copynumber: 2.8 Consensus size: 52
39137843 AGAAAAGCCC
*
39137853 AACTGTTTGAATTAGATCACCATTTTCATTGATTTATATGAACTTCTTACCT
1 AACTGTTGGAATTAGATCACCATTTTCATTGATTTATATGAACTTCTTACCT
39137905 AACTGTTGGAATTAGATCACCATTTTCATTGATTTATATGAACTTCTTACCT
1 AACTGTTGGAATTAGATCACCATTTTCATTGATTTATATGAACTTCTTACCT
39137957 AACTGTTGGAATTAGATCACCATTTTCATTGATTTATATGAAC
1 AACTGTTGGAATTAGATCACCATTTTCATTGATTTATATGAAC
39138000 AGAATATGAT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 94 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (52 bp):
AACTGTTGGAATTAGATCACCATTTTCATTGATTTATATGAACTTCTTACCT
Found at i:39154325 original size:25 final size:25
Alignment explanation
Indices: 39154296--39154375 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
39154286 GGACACACCA
*
39154296 CAGCTCGTATGAGCTTACCAAGTTG
1 CAGCTCGTATGAGCTTACCAAGTTC
** *
39154321 CAGCTCGTGA-GAGCTTACTGATTTC
1 CAGCTCGT-ATGAGCTTACCAAGTTC
39154346 CAGCTCGTATGAGCTTACCAA-TTC
1 CAGCTCGTATGAGCTTACCAAGTTC
39154370 ACAGCT
1 -CAGCT
39154376 TGCGAGAGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
24 4 0.09
25 41 0.89
26 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACCAAGTTC
Found at i:39154401 original size:50 final size:50
Alignment explanation
Indices: 39154296--39154409 Score: 124
Period size: 50 Copynumber: 2.3 Consensus size: 50
39154286 GGACACACCA
* * * * *
39154296 CAGCTCGTATGAGCTTACCAAGTTGCAGCTCGTGAGAGCTTACTGATTTC
1 CAGCTCGTATGAGCTTACCAAGTTACAGCTCGCGAGAGCATACTCAATTC
*
39154346 CAGCTCGTATGAGCTTACCAA-TTCACAGCTTGCGAGAGCATAC-CAATTC
1 CAGCTCGTATGAGCTTACCAAGTT-ACAGCTCGCGAGAGCATACTCAATTC
* *
39154395 ATAGCTCTTATGAGC
1 -CAGCTCGTATGAGC
39154410 ATACATGTAC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
49 6 0.11
50 48 0.89
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (50 bp):
CAGCTCGTATGAGCTTACCAAGTTACAGCTCGCGAGAGCATACTCAATTC
Found at i:39154409 original size:25 final size:25
Alignment explanation
Indices: 39154346--39154413 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
39154336 TACTGATTTC
* *
39154346 CAGCTCGTATGAGCTTACCAATTCA
1 CAGCTCTTATGAGCATACCAATTCA
*
39154371 CAGCT-TGCGA-GAGCATACCAATTCA
1 CAGCTCT--TATGAGCATACCAATTCA
*
39154396 TAGCTCTTATGAGCATAC
1 CAGCTCTTATGAGCATAC
39154414 ATGTACATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
24 1 0.03
25 31 0.91
26 2 0.06
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (25 bp):
CAGCTCTTATGAGCATACCAATTCA
Found at i:39158443 original size:13 final size:13
Alignment explanation
Indices: 39158425--39158451 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39158415 TTCGATGTTG
39158425 TGTTTGCAATATA
1 TGTTTGCAATATA
39158438 TGTTTGCAATATA
1 TGTTTGCAATATA
39158451 T
1 T
39158452 TCACATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TGTTTGCAATATA
Found at i:39159453 original size:43 final size:43
Alignment explanation
Indices: 39159302--39159454 Score: 125
Period size: 43 Copynumber: 3.6 Consensus size: 43
39159292 GGCACTACAA
* * * *
39159302 TGCATCATCAGATAAACTGAAGGAAA-TATATTGGCACGCATAG
1 TGCATCATCAGATATACCGAA-GAAATTATACTGGCATGCATAG
* * *
39159345 TGCATCGTCAGATGTACCGAA-CAATGTATACTGGCACT-CATAG
1 TGCATCATCAGATATACCGAAGAAAT-TATACTGGCA-TGCATAG
* * * * *
39159388 TGTATCATCAAACA-AGCTGAAGAAATTATACTAGCATGCATAG
1 TGCATCATCAGATATA-CCGAAGAAATTATACTGGCATGCATAG
*
39159431 TGCATCATCGGATATACCGAAGAA
1 TGCATCATCAGATATACCGAAGAA
39159455 TGTATATTGA
Statistics
Matches: 83, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 75 0.90
44 4 0.05
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (43 bp):
TGCATCATCAGATATACCGAAGAAATTATACTGGCATGCATAG
Found at i:39159608 original size:84 final size:85
Alignment explanation
Indices: 39159328--39159613 Score: 279
Period size: 86 Copynumber: 3.4 Consensus size: 85
39159318 CTGAAGGAAA
* * * * * * *
39159328 TATATTGGCACGCATAGTGCATCGTCAGATGTACCGAACAATGTATACTGGCACTCATAGTGTAT
1 TATACTGGCACACATAGTGCATCATCGGATGTACCGAAAAATGTATA-TGACACTCATAGTGCAT
* *
39159393 CATCAAACAAGCTGAAGA-AAT
65 CATCAGACAAGCCGAA-ACAAT
* ** * * * *
39159414 TATACTAGCATGCATAGTGCATCATCGGATATACCGAAGAATGTATATTGACTCTCATAGTACAT
1 TATACTGGCACACATAGTGCATCATCGGATGTACCGAAAAATGTATA-TGACACTCATAGTGCAT
* *
39159479 CATCGGACAAGTCGAAACAAT
65 CATCAGACAAGCCGAAACAAT
* * * * * *
39159500 TATACTGACATACATAGCGCATCATTGGATGTATCGAAAAATGTATA-GTCACTCATAGTGCATC
1 TATACTGGCACACATAGTGCATCATCGGATGTACCGAAAAATGTATATGACACTCATAGTGCATC
*
39159564 ATTAGACAAGCCGAAACAAT
66 ATCAGACAAGCCGAAACAAT
* * *
39159584 TATATTGGCACATATAGTGTATCATCGGAT
1 TATACTGGCACACATAGTGCATCATCGGAT
39159614 AAATTAAAGC
Statistics
Matches: 162, Mismatches: 37, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
84 54 0.33
85 1 0.01
86 107 0.66
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (85 bp):
TATACTGGCACACATAGTGCATCATCGGATGTACCGAAAAATGTATATGACACTCATAGTGCATC
ATCAGACAAGCCGAAACAAT
Found at i:39164711 original size:34 final size:34
Alignment explanation
Indices: 39164668--39164737 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
39164658 TCGTTTTTTA
*
39164668 AGTGTTAGGGTTTTGTTTATTTAAATTAGGGTTT
1 AGTGTTAGGGTTTTGTTTATTTAAAGTAGGGTTT
39164702 AGTGTTAGGGTTTTGTTTATTTAAAGTAGGGTTT
1 AGTGTTAGGGTTTTGTTTATTTAAAGTAGGGTTT
39164736 AG
1 AG
39164738 GGATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (34 bp):
AGTGTTAGGGTTTTGTTTATTTAAAGTAGGGTTT
Found at i:39166443 original size:18 final size:18
Alignment explanation
Indices: 39166409--39166444 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39166399 AATTTATGAG
*
39166409 ATTTTTTAAAATTTTTTA
1 ATTTTTTAAAATATTTTA
*
39166427 ATTTTTTAATATATTTTA
1 ATTTTTTAAAATATTTTA
39166445 TTTAACTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTTAAAATATTTTA
Found at i:39166493 original size:15 final size:15
Alignment explanation
Indices: 39166473--39166503 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39166463 ATATATGAAC
39166473 TGTGATGTAAGTAAT
1 TGTGATGTAAGTAAT
39166488 TGTGATGTAAGTAAT
1 TGTGATGTAAGTAAT
39166503 T
1 T
39166504 ATATCAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (15 bp):
TGTGATGTAAGTAAT
Found at i:39167964 original size:42 final size:42
Alignment explanation
Indices: 39167913--39167996 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
39167903 GGTACTCATC
39167913 GCCACTCACAGGGTATCTAAACCAGCCATCAGATTTGGTGTT
1 GCCACTCACAGGGTATCTAAACCAGCCATCAGATTTGGTGTT
*
39167955 GCCACTCACAGGGTATCTAAACGAGCCATCAGATTTGGTGTT
1 GCCACTCACAGGGTATCTAAACCAGCCATCAGATTTGGTGTT
39167997 TGAATGCTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (42 bp):
GCCACTCACAGGGTATCTAAACCAGCCATCAGATTTGGTGTT
Found at i:39168629 original size:25 final size:25
Alignment explanation
Indices: 39168595--39168644 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
39168585 CCACCGTAAG
39168595 AATAGCTAATAGAATTGACTTCTAC
1 AATAGCTAATAGAATTGACTTCTAC
39168620 AATAGCTAATAGAATTGACTTCTAC
1 AATAGCTAATAGAATTGACTTCTAC
39168645 CGAGTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (25 bp):
AATAGCTAATAGAATTGACTTCTAC
Found at i:39168897 original size:126 final size:126
Alignment explanation
Indices: 39168672--39168901 Score: 379
Period size: 126 Copynumber: 1.8 Consensus size: 126
39168662 CACTAACAAA
* *
39168672 GGTATTGGCATTTGTTATCGGTATACAAGAATCCTTAAATATTTTCCCAAATCTTCTGTCTGTTG
1 GGTATCGGCATTTGTTATCGGAATACAAGAATCCTTAAATATTTTCCCAAATCTTCTGTCTGTTG
*
39168737 AAAACCCAACTTGCTTGTAACATGACTCCTCAATGATTCCAAACTTTGTCAAAAATGAATT
66 AAAACACAACTTGCTTGTAACATGACTCCTCAATGATTCCAAACTTTGTCAAAAATGAATT
* * * *
39168798 GGTATCGGCATTTTTTATCGGAATAGAGGAATCCTTAAATATTTTCCCAAATCTTCTGTTTGTTG
1 GGTATCGGCATTTGTTATCGGAATACAAGAATCCTTAAATATTTTCCCAAATCTTCTGTCTGTTG
* *
39168863 AAAACACAACTTGCTTGTAACTTGACTCTTCAATGATTC
66 AAAACACAACTTGCTTGTAACATGACTCCTCAATGATTC
39168902 ACACGTGTTT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 95 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (126 bp):
GGTATCGGCATTTGTTATCGGAATACAAGAATCCTTAAATATTTTCCCAAATCTTCTGTCTGTTG
AAAACACAACTTGCTTGTAACATGACTCCTCAATGATTCCAAACTTTGTCAAAAATGAATT
Found at i:39170601 original size:50 final size:51
Alignment explanation
Indices: 39170530--39170627 Score: 153
Period size: 50 Copynumber: 1.9 Consensus size: 51
39170520 TTCATTAAAA
* *
39170530 GATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGACATAATTTAT
1 GATGCAAACTTTAACTAACATGAGAGTAACATAATGCATGACATAATTTAT
* *
39170581 GATGCAATC-TTAACTAACATGAGAGTAACATAATGCATGTCATAATT
1 GATGCAAACTTTAACTAACATGAGAGTAACATAATGCATGACATAATT
39170628 AAAAGATGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 35 0.81
51 8 0.19
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (51 bp):
GATGCAAACTTTAACTAACATGAGAGTAACATAATGCATGACATAATTTAT
Found at i:39171218 original size:31 final size:31
Alignment explanation
Indices: 39171125--39171220 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
39171115 GGCAAATTAC
*
39171125 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
39171156 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
39171188 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
39171219 AA
1 AA
39171221 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:39173133 original size:35 final size:35
Alignment explanation
Indices: 39173059--39173182 Score: 115
Period size: 35 Copynumber: 3.6 Consensus size: 35
39173049 TAGAAACACG
* * * * *
39173059 AGGATGATGAGTGTGGTGACCCGA-TAAAAATATA
1 AGGATGACGAATGTGGCGACCCAACTAAAAACATA
* * *
39173093 AGGATGACGAATGTGGCAACCCAACTAGAAACATG
1 AGGATGACGAATGTGGCGACCCAACTAAAAACATA
* * * *
39173128 AGGATGATGGATGTGGCGGCCCAACCAAAAACATA
1 AGGATGACGAATGTGGCGACCCAACTAAAAACATA
* *
39173163 AGGATGACGCATATGGCGAC
1 AGGATGACGAATGTGGCGAC
39173183 TTGGCCAGAA
Statistics
Matches: 70, Mismatches: 19, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
34 19 0.27
35 51 0.73
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (35 bp):
AGGATGACGAATGTGGCGACCCAACTAAAAACATA
Found at i:39173239 original size:35 final size:35
Alignment explanation
Indices: 39173128--39173264 Score: 96
Period size: 35 Copynumber: 3.9 Consensus size: 35
39173118 TAGAAACATG
* * ** * * *
39173128 AGGATGATGGATGTGGCGGCCCAACCAAAAACATA
1 AGGATGATGGATGTGGCGACTCGGCCAGAAATACA
* * * * * *
39173163 AGGATGACGCATATGGCGACTTGGCCAGAAACATA
1 AGGATGATGGATGTGGCGACTCGGCCAGAAATACA
* *
39173198 ATGATGATAGG-TGTGGCGACTCGGCCAGAAATACG
1 AGGATGAT-GGATGTGGCGACTCGGCCAGAAATACA
* * *
39173233 AGGATGATGGATGTGGTGAGTCGGCCAAAAAT
1 AGGATGATGGATGTGGCGACTCGGCCAGAAAT
39173265 GTAACACCCT
Statistics
Matches: 79, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
34 2 0.03
35 76 0.96
36 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.18
Consensus pattern (35 bp):
AGGATGATGGATGTGGCGACTCGGCCAGAAATACA
Found at i:39173649 original size:18 final size:17
Alignment explanation
Indices: 39173618--39173651 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39173608 CTCATAACAA
*
39173618 CATAAAACATGAGTTCG
1 CATAAAACACGAGTTCG
39173635 CATAATAACACGAGTTC
1 CATAA-AACACGAGTTC
39173652 ACAAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (17 bp):
CATAAAACACGAGTTCG
Found at i:39176253 original size:15 final size:16
Alignment explanation
Indices: 39176228--39176259 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
39176218 TTGGATTGAA
39176228 TTGATATATATATATT
1 TTGATATATATATATT
39176244 TTGAATATATATATAT
1 TTG-ATATATATATAT
39176260 GCAAACATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TTGATATATATATATT
Found at i:39177599 original size:23 final size:23
Alignment explanation
Indices: 39177565--39177615 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
39177555 GTGTGAGACA
*
39177565 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
39177588 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
39177611 AGTAA
1 TGTAA
39177616 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:39183957 original size:27 final size:26
Alignment explanation
Indices: 39183927--39183979 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
39183917 CCCAGTTCGC
*
39183927 CAAACCAACTGGCGAACCCTAACTTGT
1 CAAACCAACTGGCGAACAC-AACTTGT
* *
39183954 CAAACCAATTGTCGAACACAACTTGT
1 CAAACCAACTGGCGAACACAACTTGT
39183980 AATGAACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.36, C:0.30, G:0.13, T:0.21
Consensus pattern (26 bp):
CAAACCAACTGGCGAACACAACTTGT
Found at i:39184274 original size:35 final size:35
Alignment explanation
Indices: 39184148--39184316 Score: 108
Period size: 35 Copynumber: 4.9 Consensus size: 35
39184138 GGATGTTACA
** **
39184148 AGAAACATGAGGATGACGGGTGTGGCAACCCAACC
1 AGAAACACAAGGATGACGGGTGTGGTGACCCAACC
* * ** * ***
39184183 AGAAATACAAGAATGACGATTGTGGCGA-TTGACC
1 AGAAACACAAGGATGACGGGTGTGGTGACCCAACC
* ** * *
39184217 A-AAACATAAGGACAATGAGTGTGGTGACCCAACC
1 AGAAACACAAGGATGACGGGTGTGGTGACCCAACC
* ** ***
39184251 ATAAACATGAGGATGACGGGTGTGACAACCCAACC
1 AGAAACACAAGGATGACGGGTGTGGTGACCCAACC
*
39184286 AGAAACACAATGATGACGGGTGTGGTGACCC
1 AGAAACACAAGGATGACGGGTGTGGTGACCC
39184317 GATTAGAAAC
Statistics
Matches: 96, Mismatches: 36, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
33 18 0.19
34 8 0.08
35 70 0.73
ACGTcount: A:0.37, C:0.20, G:0.28, T:0.15
Consensus pattern (35 bp):
AGAAACACAAGGATGACGGGTGTGGTGACCCAACC
Found at i:39188161 original size:61 final size:61
Alignment explanation
Indices: 39188054--39188194 Score: 138
Period size: 61 Copynumber: 2.3 Consensus size: 61
39188044 AACACTAAAT
* * ** * * * *
39188054 AGGAAAACCTTTGTTGTGAGTATTGGATGTAAAGGACAACCTTTGTGGAAAAAATTTGGAC
1 AGGAAAGCCTTTGTAGCAAGTACTGGATGTAAAGGACAACCATTGTGGAAAAAATCTGGAA
* *** **
39188115 AGGAAAGCCTTTGTGGCAAGTACTGGATGTAAAGGACTGTCATTGTGGTGAAAATCTGGAA
1 AGGAAAGCCTTTGTAGCAAGTACTGGATGTAAAGGACAACCATTGTGGAAAAAATCTGGAA
**
39188176 AGGTGAGCCTTTGTAGCAA
1 AGGAAAGCCTTTGTAGCAA
39188195 TCTCTGTTTA
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.28
Consensus pattern (61 bp):
AGGAAAGCCTTTGTAGCAAGTACTGGATGTAAAGGACAACCATTGTGGAAAAAATCTGGAA
Found at i:39188271 original size:29 final size:27
Alignment explanation
Indices: 39188226--39188297 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
39188216 GTGGAAAATT
* *
39188226 TCTA-AAAGGAAATGCCTTTGTTGCAATC
1 TCTATAAAGGAAA-GCCTCTGTGGCAA-C
39188254 TCTATCAAAGGAAAGCCTCTGTGGCAAC
1 TCTAT-AAAGGAAAGCCTCTGTGGCAAC
* *
39188282 TTTGTAAAGGAAAGCC
1 TCTATAAAGGAAAGCC
39188298 CTTATGGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
27 11 0.29
28 8 0.21
29 11 0.29
30 8 0.21
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (27 bp):
TCTATAAAGGAAAGCCTCTGTGGCAAC
Found at i:39190879 original size:19 final size:20
Alignment explanation
Indices: 39190850--39190890 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
39190840 ATAAATATTC
39190850 AAAATATTTTAAAAAATTAA
1 AAAATATTTTAAAAAATTAA
*
39190870 AAAATA-TTTAAAATATTAA
1 AAAATATTTTAAAAAATTAA
39190889 AA
1 AA
39190891 TTGATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATATTTTAAAAAATTAA
Found at i:39190973 original size:35 final size:33
Alignment explanation
Indices: 39190861--39190996 Score: 112
Period size: 35 Copynumber: 3.9 Consensus size: 33
39190851 AAATATTTTA
* * *
39190861 AAAAATTA-AAAAATATTTAAAATATTAAAATTGAT
1 AAAAATTATAAAAA-ATATAAAATAATAAAA-T-CT
* ** *
39190896 ATAAAATTATAAAAATTATAAAATAATAATTTGT
1 A-AAAATTATAAAAAATATAAAATAATAAAATCT
* *
39190930 AAATATTATAAAAACATAAAAAACTAATAAAATCT
1 AAAAATTATAAAAA-ATATAAAA-TAATAAAATCT
39190965 AAAAATTATAAAAAATTATAAAATTAATAAAA
1 AAAAATTATAAAAAA-TATAAAA-TAATAAAA
39190997 CATATTTAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 10
0.76 0.14 0.09
Matches are distributed among these distances:
33 12 0.15
34 9 0.11
35 37 0.46
36 18 0.22
37 5 0.06
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (33 bp):
AAAAATTATAAAAAATATAAAATAATAAAATCT
Found at i:39191017 original size:21 final size:20
Alignment explanation
Indices: 39190970--39191030 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
39190960 AATCTAAAAA
39190970 TTATAAAAA-ATTATAAAA-T
1 TTATAAAAATATT-TAAAATT
*
39190989 TAATAAAACATATTTAAAATT
1 TTATAAAA-ATATTTAAAATT
*
39191010 TTATAAAAATGTATTAAAATT
1 TTATAAAAATAT-TTAAAATT
39191031 CTTAAAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 7 0.20
20 9 0.26
21 19 0.54
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TTATAAAAATATTTAAAATT
Found at i:39191038 original size:21 final size:19
Alignment explanation
Indices: 39190966--39191101 Score: 72
Period size: 19 Copynumber: 7.2 Consensus size: 19
39190956 ATAAAATCTA
*
39190966 AAAATTATAAAAAATTA-T
1 AAAATTTTAAAAAATTATT
* *
39190984 AAAATTAATAAAACA-TATTT
1 AAAATT-TTAAAAAATTA-TT
39191004 AAAATTTTATAAAAATGTATT
1 AAAATTTTA-AAAAAT-TATT
*
39191025 AAAATTCTTAAAAACTTA--
1 AAAATT-TTAAAAAATTATT
** *
39191043 AAAATCATAAAAAATAATT
1 AAAATTTTAAAAAATTATT
*
39191062 AAAATATT--AAAATTGATAT
1 AAAATTTTAAAAAATT-AT-T
*
39191081 AAAATTAT-AAAAATTA-T
1 AAAATTTTAAAAAATTATT
39191098 AAAA
1 AAAA
39191102 AAATCGCAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
17 18 0.19
18 15 0.16
19 23 0.25
20 19 0.20
21 13 0.14
22 5 0.05
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (19 bp):
AAAATTTTAAAAAATTATT
Found at i:39191100 original size:28 final size:28
Alignment explanation
Indices: 39190966--39191101 Score: 84
Period size: 28 Copynumber: 4.8 Consensus size: 28
39190956 ATAAAATCTA
*
39190966 AAAATTATAAAAAATTATAAAATTAATA-
1 AAAATTAT-AAAAATTATAAAATTGATAT
* * *
39190994 AAACATATTTAAAATTTTATAAAAATG-TATT
1 AAA-AT-TATAAAA-ATTATAAAATTGATA-T
* * *
39191025 AAAATTCTTAAAAACTTA-AAAA-TCATAA
1 AAAATT-ATAAAAA-TTATAAAATTGATAT
* *
39191053 AAAATAATTAAAA-TATTAAAATTGATAT
1 AAAATTATAAAAATTA-TAAAATTGATAT
39191081 AAAATTATAAAAATTATAAAA
1 AAAATTATAAAAATTATAAAA
39191102 AAATCGCAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
25 2 0.02
27 9 0.11
28 29 0.35
29 17 0.21
30 22 0.27
31 3 0.04
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (28 bp):
AAAATTATAAAAATTATAAAATTGATAT
Found at i:39191105 original size:11 final size:9
Alignment explanation
Indices: 39190861--39191102 Score: 103
Period size: 9 Copynumber: 26.6 Consensus size: 9
39190851 AAATATTTTA
39190861 AAAAATTA-
1 AAAAATTAT
39190869 AAAAA-TATT
1 AAAAATTA-T
*
39190878 TAAAA-TAT
1 AAAAATTAT
*
39190886 TAAAATTGAT
1 AAAAATT-AT
39190896 ATAAAATTAT
1 A-AAAATTAT
39190906 AAAAATTAT
1 AAAAATTAT
39190915 -AAAA-TA-
1 AAAAATTAT
* * *
39190921 ATAATTTGT
1 AAAAATTAT
*
39190930 AAATATTAT
1 AAAAATTAT
*
39190939 AAAAA-CAT
1 AAAAATTAT
39190947 AAAAA--ACT
1 AAAAATTA-T
* *
39190955 AATAAAATCT
1 AA-AAATTAT
39190965 AAAAATTAT
1 AAAAATTAT
39190974 AAAAAATTAT
1 -AAAAATTAT
39190984 -AAAATTAAT
1 AAAAATT-AT
*
39190993 AAAACATATTT
1 AAAA-AT-TAT
*
39191004 AAAATTTTAT
1 AAAA-ATTAT
39191014 AAAAATGTAT
1 AAAAAT-TAT
* *
39191024 TAAAATTCTT
1 AAAAATT-AT
*
39191034 AAAAACT-T
1 AAAAATTAT
*
39191042 AAAAATCAT
1 AAAAATTAT
*
39191051 AAAAAATAAT
1 -AAAAATTAT
*
39191061 TAAAA-TAT
1 AAAAATTAT
*
39191069 TAAAATTGAT
1 AAAAATT-AT
39191079 ATAAAATTAT
1 A-AAAATTAT
39191089 AAAAATTAT
1 AAAAATTAT
39191098 AAAAA
1 AAAAA
39191103 AATCGCAATA
Statistics
Matches: 181, Mismatches: 29, Indels: 47
0.70 0.11 0.18
Matches are distributed among these distances:
7 7 0.04
8 45 0.25
9 55 0.30
10 53 0.29
11 20 0.11
12 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:39191582 original size:27 final size:28
Alignment explanation
Indices: 39191534--39191607 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
39191524 GTTTATATCA
* * *
39191534 ATTTTTATTTTTTTTTATTTTTAAA-A-
1 ATTTTAATATTTTTTTAATTTTAAATAG
39191560 ATTTTAATACTTTTTTTAATTTTAAATAG
1 ATTTTAATA-TTTTTTTAATTTTAAATAG
*
39191589 GTTTTAATA-TTTTTTAATT
1 ATTTTAATATTTTTTTAATT
39191608 ATTATATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 7 0.17
27 25 0.61
28 1 0.02
29 8 0.20
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (28 bp):
ATTTTAATATTTTTTTAATTTTAAATAG
Found at i:39191655 original size:17 final size:17
Alignment explanation
Indices: 39191614--39191670 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
39191604 AATTATTATA
*
39191614 TTTT-ATATTTTA-CAA
1 TTTTAATATTTTACCAT
*
39191629 TTTTAATAATTTTATATCAT
1 TTTTAAT-A-TTT-TACCAT
39191649 TTTTAATATTTTACCAT
1 TTTTAATATTTTACCAT
39191666 TTTTA
1 TTTTA
39191671 TGATTTGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
15 4 0.11
16 2 0.06
17 11 0.31
18 6 0.17
19 3 0.09
20 9 0.26
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAATATTTTACCAT
Found at i:39197939 original size:120 final size:120
Alignment explanation
Indices: 39197801--39198055 Score: 501
Period size: 120 Copynumber: 2.1 Consensus size: 120
39197791 ATTATAAAAT
*
39197801 ATTTATTTATAAAAAAGTTACAGTTAAGAAATCTGATATAACTTATTTATGTGTCTATATTATAT
1 ATTTATTTATAAAAAAGTTACAGCTAAGAAATCTGATATAACTTATTTATGTGTCTATATTATAT
39197866 ATTATAAAAATAATATATTTATTCGTAAAAAATGTTATAGCTTTTTTTTATCATA
66 ATTATAAAAATAATATATTTATTCGTAAAAAATGTTATAGCTTTTTTTTATCATA
39197921 ATTTATTTATAAAAAAGTTACAGCTAAGAAATCTGATATAACTTATTTATGTGTCTATATTATAT
1 ATTTATTTATAAAAAAGTTACAGCTAAGAAATCTGATATAACTTATTTATGTGTCTATATTATAT
39197986 ATTATAAAAATAATATATTTATTCGTAAAAAATGTTATAGCTTTTTTTTATCATA
66 ATTATAAAAATAATATATTTATTCGTAAAAAATGTTATAGCTTTTTTTTATCATA
39198041 ATTTATTTATAAAAA
1 ATTTATTTATAAAAA
39198056 GTAACTTTCT
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 134 1.00
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (120 bp):
ATTTATTTATAAAAAAGTTACAGCTAAGAAATCTGATATAACTTATTTATGTGTCTATATTATAT
ATTATAAAAATAATATATTTATTCGTAAAAAATGTTATAGCTTTTTTTTATCATA
Found at i:39198887 original size:46 final size:46
Alignment explanation
Indices: 39198834--39198925 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
39198824 AACAACAAAT
39198834 TCAAGTGTTAGAAGGAATTCATCACCCGAATCAAAGGTCCTGCTGA
1 TCAAGTGTTAGAAGGAATTCATCACCCGAATCAAAGGTCCTGCTGA
39198880 TCAAGTGTTAGAAGGAATTCATCACCCGAATCAAAGGTCCTGCTGA
1 TCAAGTGTTAGAAGGAATTCATCACCCGAATCAAAGGTCCTGCTGA
39198926 ATTTGATATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (46 bp):
TCAAGTGTTAGAAGGAATTCATCACCCGAATCAAAGGTCCTGCTGA
Found at i:39201483 original size:4 final size:4
Alignment explanation
Indices: 39201474--39201534 Score: 122
Period size: 4 Copynumber: 15.2 Consensus size: 4
39201464 TTTGTTTTTG
39201474 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
39201522 CATA CATA CATA C
1 CATA CATA CATA C
39201535 TTTAGTTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:39201857 original size:4 final size:4
Alignment explanation
Indices: 39201848--39201885 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
39201838 AAAAACTAAA
39201848 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
39201886 GTTGTTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:39206588 original size:27 final size:27
Alignment explanation
Indices: 39206550--39206603 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
39206540 TTTGGGGTTA
*
39206550 GTAGAAATAACTAGTGTTTATAAGTCT
1 GTAGAAATAACTAGTGCTTATAAGTCT
39206577 GTAGAAATAACTAGTGCTTATAAGTCT
1 GTAGAAATAACTAGTGCTTATAAGTCT
39206604 ACTAGTAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (27 bp):
GTAGAAATAACTAGTGCTTATAAGTCT
Found at i:39223434 original size:50 final size:49
Alignment explanation
Indices: 39223372--39223501 Score: 163
Period size: 50 Copynumber: 2.6 Consensus size: 49
39223362 AGGTCCCATG
**
39223372 TAAGACCATGTCTGGAACATGGCATTGGCACCAAGATAAGAGGTCTCCC-A
1 TAAGACCATGTCTGGAACATGGCATTGGCACC--GATAAGAGAACTCCCAA
*
39223422 TAAGACCATGTCTGGAACATGGCATTGGCACCGATATGAGAACTCCCATA
1 TAAGACCATGTCTGGAACATGGCATTGGCACCGATAAGAGAACTCCCA-A
* * * *
39223472 TAAGACTATATCTGGGATATGGCATTGGCA
1 TAAGACCATGTCTGGAACATGGCATTGGCA
39223502 GTATAGAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
48 12 0.17
50 59 0.83
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (49 bp):
TAAGACCATGTCTGGAACATGGCATTGGCACCGATAAGAGAACTCCCAA
Found at i:39223537 original size:49 final size:49
Alignment explanation
Indices: 39223365--39223550 Score: 155
Period size: 50 Copynumber: 3.8 Consensus size: 49
39223355 GGTAAAGAGG
* * * ***
39223365 TCCCATGTAAGACCATGTCTGGAACATGGCATTGGCACCAAGATAAGAGGTC
1 TCCCATATAAGACCATGTCTGGGACATGGCATTGGCA-C--GATATGAAAAC
* *
39223417 TCCC--ATAAGACCATGTCTGGAACATGGCATTGGCACCGATATGAGAAC
1 TCCCATATAAGACCATGTCTGGGACATGGCATTGGCA-CGATATGAAAAC
* * *
39223465 TCCCATATAAGACTATATCTGGGATATGGCATTGGCA-G-TATAGAAAAC
1 TCCCATATAAGACCATGTCTGGGACATGGCATTGGCACGATAT-GAAAAC
* * * *
39223513 ATCCCATGTAAGACCATGTATGGGACATGACTTTGGCA
1 -TCCCATATAAGACCATGTCTGGGACATGGCATTGGCA
39223551 TGCTATTATC
Statistics
Matches: 114, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
47 3 0.03
48 18 0.16
49 30 0.26
50 59 0.52
52 4 0.04
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (49 bp):
TCCCATATAAGACCATGTCTGGGACATGGCATTGGCACGATATGAAAAC
Found at i:39226772 original size:19 final size:19
Alignment explanation
Indices: 39226748--39226786 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
39226738 TGCAGGAATT
39226748 AACTGATAAAGGTTTTGCA
1 AACTGATAAAGGTTTTGCA
39226767 AACTGATAAAGGTTTTGCA
1 AACTGATAAAGGTTTTGCA
39226786 A
1 A
39226787 GGCCTAGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (19 bp):
AACTGATAAAGGTTTTGCA
Found at i:39230722 original size:50 final size:49
Alignment explanation
Indices: 39230665--39230820 Score: 161
Period size: 50 Copynumber: 3.1 Consensus size: 49
39230655 AAACATAGCG
*
39230665 TTGGCACCGAGATGAAAGGTCGCATGTAAGACCATATCTTGGACATGGCA
1 TTGGCACCGAGATGAAAGGTC-CATGTAAGACCATATCTAGGACATGGCA
* ** * * *
39230715 TTGGCACCGAGATGAGAGGTTCCCCGTAAGACCATGTCTGGGACATGACA
1 TTGGCACCGAGATGAAAGG-TCCATGTAAGACCATATCTAGGACATGGCA
* * * * *
39230765 TGGGGACCGATATGAGAA-CTCCCATGTAAGACCATATCTAGGATATGGCA
1 TTGGCACCGAGATGA-AAGGT-CCATGTAAGACCATATCTAGGACATGGCA
39230815 TTGGCA
1 TTGGCA
39230821 GTACAGAAAA
Statistics
Matches: 84, Mismatches: 19, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
49 1 0.01
50 80 0.95
51 3 0.04
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (49 bp):
TTGGCACCGAGATGAAAGGTCCATGTAAGACCATATCTAGGACATGGCA
Found at i:39236795 original size:28 final size:28
Alignment explanation
Indices: 39236773--39236830 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
39236763 TGTTTAGGGT
39236773 TTGAGTTTAATGTTTAAGAGTTTGGAGG
1 TTGAGTTTAATGTTTAAGAGTTTGGAGG
* *
39236801 TTGGGTTTAGTGTTTAATGA-TTTGG-GG
1 TTGAGTTTAATGTTTAA-GAGTTTGGAGG
39236828 TTG
1 TTG
39236831 TGGGTTCAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 5 0.19
28 20 0.74
29 2 0.07
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (28 bp):
TTGAGTTTAATGTTTAAGAGTTTGGAGG
Found at i:39237633 original size:5 final size:5
Alignment explanation
Indices: 39237625--39237667 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
39237615 GGAAATATGA
39237625 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
39237668 GATGCAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:39238573 original size:13 final size:13
Alignment explanation
Indices: 39238555--39238597 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
39238545 TAGAATTTTC
39238555 CTAAATATTATCA
1 CTAAATATTATCA
*
39238568 CTAAATA--AT-T
1 CTAAATATTATCA
39238578 CTAAATATTATCA
1 CTAAATATTATCA
39238591 CTAAATA
1 CTAAATA
39238598 ATTCTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:39238581 original size:23 final size:23
Alignment explanation
Indices: 39238555--39238606 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
39238545 TAGAATTTTC
39238555 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
39238578 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
39238601 CTAAAT
1 CTAAAT
39238607 TTAAAAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.38
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:39238619 original size:23 final size:23
Alignment explanation
Indices: 39238555--39238619 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
39238545 TAGAATTTTC
** *
39238555 CTAAATATTATCACTAAATAATT
1 CTAAATATTAAAAATAAATAATT
** *
39238578 CTAAATATTATCACTAAATAATT
1 CTAAATATTAAAAATAAATAATT
39238601 CTAAAT-TTAAAAATCAAAT
1 CTAAATATTAAAAAT-AAAT
39238620 TTAAACTAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 5 0.13
23 33 0.87
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTAAAAATAAATAATT
Found at i:39242985 original size:20 final size:19
Alignment explanation
Indices: 39242937--39242985 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
39242927 AAAATAAAAT
*
39242937 AAAATAAAAATAGATTCAA
1 AAAATAAAAATAAATTCAA
* *
39242956 AAATACAAAAATAAATTTAA
1 AAA-ATAAAAATAAATTCAA
39242976 GAAAATAAAA
1 -AAAATAAAA
39242986 CAAATGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.12
20 18 0.75
21 3 0.12
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (19 bp):
AAAATAAAAATAAATTCAA
Found at i:39243829 original size:13 final size:13
Alignment explanation
Indices: 39243811--39243853 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
39243801 TAGATTTTTC
39243811 CTAAATATTATCA
1 CTAAATATTATCA
39243824 CTAAATA--ATC-
1 CTAAATATTATCA
39243834 CTAAATATTATCA
1 CTAAATATTATCA
39243847 CTAAATA
1 CTAAATA
39243854 ATTCAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 3 0.11
13 14 0.52
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:39243836 original size:23 final size:23
Alignment explanation
Indices: 39243809--39243855 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
39243799 GCTAGATTTT
39243809 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
39243832 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
39243855 T
1 T
39243856 TCAAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:39243862 original size:23 final size:23
Alignment explanation
Indices: 39243813--39243862 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
39243803 GATTTTTCCT
*
39243813 AAATATTATCACTAAATAATCCT
1 AAATATTATCACTAAATAATCCA
*
39243836 AAATATTATCACTAAATAATTCA
1 AAATATTATCACTAAATAATCCA
39243859 AAAT
1 AAAT
39243863 TTAAAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATATTATCACTAAATAATCCA
Found at i:39250979 original size:3 final size:3
Alignment explanation
Indices: 39250971--39251025 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
39250961 AAAATTACAA
39250971 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
39251019 AAG AAG A
1 AAG AAG A
39251026 CTAAATTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39255746 original size:72 final size:72
Alignment explanation
Indices: 39255662--39255800 Score: 217
Period size: 72 Copynumber: 1.9 Consensus size: 72
39255652 CCAAATGAAT
* *
39255662 ATTAAAACTAAATAAAATCTGTTTGGGGATTTATTCCCGCTGTTTC-ACAAATTTTATTCGATTT
1 ATTAAAACTAAATAAAATCCGTTTGGGGATTTATTCCCGCTG-TTCAACAAATTTTATTCCATTT
39255726 TTTTCCAA
65 TTTTCCAA
* * *
39255734 ATTAAAAGTAAATAAAATCCGTTTTGGGATTTATTCCCGCTGTTCAACGAATTTTATTCCATTTT
1 ATTAAAACTAAATAAAATCCGTTTGGGGATTTATTCCCGCTGTTCAACAAATTTTATTCCATTTT
39255799 TT
66 TT
39255801 ATTATTTCTA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 3 0.05
72 58 0.95
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (72 bp):
ATTAAAACTAAATAAAATCCGTTTGGGGATTTATTCCCGCTGTTCAACAAATTTTATTCCATTTT
TTTCCAA
Found at i:39255940 original size:89 final size:89
Alignment explanation
Indices: 39255734--39256231 Score: 498
Period size: 89 Copynumber: 5.7 Consensus size: 89
39255724 TTTTTTCCAA
* * * ** * *
39255734 ATTAAAAGT-AAATAAAATCCGTTTTGGGATTTATTCCCGCTGTTCAACGAATTTTATTCC-ATT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCTACCGTTCAACGGATTTTATTCCAATT
* *** *
39255797 TT--TTATTATTTCTAAATGGGA-A
66 TTGATT-TTATTTCCAAAAACGAGT
* * * * * **
39255819 ATTAAAGTT-AAATAAAATTTGTTTCAGAATTTATTCCTATCGTTCAATAGATTTTATTCCAATT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCTACCGTTCAACGGATTTTATTCCAATT
39255883 TTGATTTTATTTCCAAAAACGAGT
66 TTGATTTTATTTCCAAAAACGAGT
39255907 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCC-AGCCGTTCAACGGATTTTATTCCAAT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCTA-CCGTTCAACGGATTTTATTCCAAT
* **
39255971 TTTCATTTTATTTTTAAAAACGAGT
65 TTTGATTTTATTTCCAAAAACGAGT
* * *
39255996 ATTAAAATTAAAATAAAATCTGTTTCGGAATTTATTCAC-GCCGTTCAACGAATTTTATTCCAAT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTC-CTACCGTTCAACGGATTTTATTCCAAT
* *
39256060 TTTGGTTTTATTTCCAAAAATGAGT
65 TTTGATTTTATTTCCAAAAACGAGT
* * *
39256085 ATTAAAATAAAAATAAAATCTGTTTCGAGATTTATT-CTCACCGTTCAACGGA-TTTATTAC-AT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCT-ACCGTTCAACGGATTTTATTCCAAT
* * * *
39256147 TTTGATTTTGTTGCCAAAAACAAGAA
65 TTTGATTTTATTTCCAAAAACGAG-T
* ** * * *
39256173 ATTAAAATT-AAATAAAATCTGTTCCAAGATTTATTCCTGCCGTTTAACAAGATTTTATT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCTACCGTTCAAC-GGATTTTATT
39256232 TGATTTTATT
Statistics
Matches: 345, Mismatches: 55, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
85 46 0.13
86 5 0.01
87 66 0.19
88 30 0.09
89 197 0.57
90 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (89 bp):
ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCTACCGTTCAACGGATTTTATTCCAATT
TTGATTTTATTTCCAAAAACGAGT
Found at i:39256071 original size:178 final size:175
Alignment explanation
Indices: 39255734--39256231 Score: 571
Period size: 178 Copynumber: 2.8 Consensus size: 175
39255724 TTTTTTCCAA
* * * * * *
39255734 ATTAAAAGT-AAATAAAATCCGTTTTGGGATTTATTCCCGCTGTTCAACGAATTTTATTCCATTT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCAGCCGTTCAACGGATTTTATTCCATTT
*** * * *
39255798 T-TTATTATTTCTAAATGGGA-AATTAAAGTTAAATAAAATTTGTTTCAGAATTTATTCCTATCG
66 TATT-TTATTTCTAAAAACGAGAATTAAAATTAAATAAAATCTGTTTCAGAATTTATTCCTACCG
*
39255861 TTCAATAGATTTTATTCCAATTTTGATTTTATTTCCAAAAACGAGT
130 TTCAAGAGATTTTATTCCAATTTTGATTTTATTTCCAAAAACGAGT
39255907 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCAGCCGTTCAACGGATTTTATTCCAATT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCAGCCGTTCAACGGATTTTATTCC-ATT
* * * *
39255972 TTCATTTTATTTTTAAAAACGAGTATTAAAATTAAAATAAAATCTGTTTCGGAATTTATTCAC-G
65 TT-ATTTTATTTCTAAAAACGAGAATTAAAATT-AAATAAAATCTGTTTCAGAATTTATTC-CTA
* *
39256036 CCGTTCAACGA-ATTTTATTCCAATTTTGGTTTTATTTCCAAAAATGAGT
127 CCGTTCAA-GAGATTTTATTCCAATTTTGATTTTATTTCCAAAAACGAGT
* * *
39256085 ATTAAAATAAAAATAAAATCTGTTTCGAGATTTATTCTCA-CCGTTCAACGGA-TTTATTACATT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTC-CAGCCGTTCAACGGATTTTATTCCATT
* * * * * *
39256148 TTGATTTTGTTGCCAAAAACAAGAAATTAAAATTAAATAAAATCTGTTCCA-AGATTTATTCCTG
65 TT-ATTTTATTTCTAAAAACGAG-AATTAAAATTAAATAAAATCTGTTTCAGA-ATTTATTCCTA
* *
39256212 CCGTTTAACAAGATTTTATT
127 CCGTTCAA-GAGATTTTATT
39256232 TGATTTTATT
Statistics
Matches: 279, Mismatches: 33, Indels: 22
0.84 0.10 0.07
Matches are distributed among these distances:
173 8 0.03
174 46 0.16
175 7 0.03
176 65 0.23
177 34 0.12
178 115 0.41
179 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (175 bp):
ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCAGCCGTTCAACGGATTTTATTCCATTT
TATTTTATTTCTAAAAACGAGAATTAAAATTAAATAAAATCTGTTTCAGAATTTATTCCTACCGT
TCAAGAGATTTTATTCCAATTTTGATTTTATTTCCAAAAACGAGT
Found at i:39256356 original size:167 final size:165
Alignment explanation
Indices: 39256177--39256501 Score: 472
Period size: 167 Copynumber: 2.0 Consensus size: 165
39256167 CAAGAAATTA
* ** *
39256177 AAATTAAATAAAATCTGTTCCAAGATTTATTCCTGCCGTTTAACAAGATTTTATTTGATTTTATT
1 AAATTAAATAAAATCTGTTCCAAGATTTATCCCCACCGTTTAACAAGATTTTATTTGATTTAATT
* * * * *
39256242 TTGTTTCTAAATTAGAATTAAATTAAATTAAATCTGTTTCAAGATATATT-CTTGTCGTTTAACA
66 TTATTTCTAAATTAGAATTAAATTAAATAAAATATGTTTCAAGAT-T-TTCCCT-CCGTTTAACA
* *
39256306 AGATTTTATTTGATTTTATTTTGTTTCCAAATTAGAAT
128 AGATTTTATTCGATATTATTTTGTTTCCAAATTAGAAT
*** *
39256344 AAATTAAATAAAATCTGTTTTGAGATTTATCCCCACCGTTTAACAAGATTTTATTTTATTTAATT
1 AAATTAAATAAAATCTGTTCCAAGATTTATCCCCACCGTTTAACAAGATTTTATTTGATTTAATT
39256409 TTATTTCTAAATTAGAATTAAATTAAATAAAATATGTTTCAAGATTTTCCCTCCGTTTAACAAGA
66 TTATTTCTAAATTAGAATTAAATTAAATAAAATATGTTTCAAGATTTTCCCTCCGTTTAACAAGA
*
39256474 TTTTATTCGATATTGTTTTGTTTCCAAA
131 TTTTATTCGATATTATTTTGTTTCCAAA
39256502 CAAAAACGTA
Statistics
Matches: 141, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
165 39 0.28
166 3 0.02
167 99 0.70
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (165 bp):
AAATTAAATAAAATCTGTTCCAAGATTTATCCCCACCGTTTAACAAGATTTTATTTGATTTAATT
TTATTTCTAAATTAGAATTAAATTAAATAAAATATGTTTCAAGATTTTCCCTCCGTTTAACAAGA
TTTTATTCGATATTATTTTGTTTCCAAATTAGAAT
Found at i:39256399 original size:83 final size:84
Alignment explanation
Indices: 39255733--39256580 Score: 479
Period size: 89 Copynumber: 9.9 Consensus size: 84
39255723 TTTTTTTCCA
* * *** * * * **
39255733 AATTAAAAGTAAATAAAATCCGTTTTGGGATTTATTCCCGCTGTTCAACGA-ATTTTATTCCATT
1 AATT-AAATTAAATAAAATCTGTTTCAAGATTTATTCCCGCCGTTTAACAAGATTTTATTTGATT
* * **
39255797 TT-TTATTATTTCTAAATGGG
65 TTATT-TTGTTTCCAAATTAG
* *** * * **
39255817 AAATTAAAGTTAAATAAAATTTGTTTC-AGAATTTATTCCTATCGTTCAA-TAGATTTTATTCCA
1 -AATTAAA-TTAAATAAAATCTGTTTCAAG-ATTTATTCCCGCCGTTTAACAAGATTTTATT-TG
* *
39255880 ATTTTGATTTTATTTCCAAA-AACG
62 ATTTT-ATTTTGTTTCCAAATTA-G
** * * * *
39255904 AGTATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCAGCCGTTCAAC-GGATTTTATTCC
1 A--ATT-AAATT-AAATAAAATCTGTTTCAAGATTTATTCCCGCCGTTTAACAAGATTTTATT-T
* * ** *
39255968 AATTTTCATTTTATTTTTAAA-AACG
61 GATTTT-ATTTTGTTTCCAAATTA-G
* * * *
39255993 AGTATTAAAATTAAAATAAAATCTGTTTC-GGAATTTATTCACGCCGTTCAACGA-ATTTTATTC
1 A--ATT-AAATT-AAATAAAATCTGTTTCAAG-ATTTATTCCCGCCGTTTAACAAGATTTTATT-
** * * *
39256056 CAATTTTGGTTTTATTTCCAAAAATGAG
60 TGATTTT-ATTTTGTTTCC--AAATTAG
* * * * * * * **
39256084 TATTAAAATAAAAATAAAATCTGTTTCGAGATTTATTCTCACCGTTCAAC-GGA-TTTATTACAT
1 AATT-AAAT-TAAATAAAATCTGTTTCAAGATTTATTCCCGCCGTTTAACAAGATTTTATTTGAT
* **
39256147 TTTGATTTTGTTGCCAAAAACAAG
64 TTT-ATTTTGTTTCC--AAATTAG
* *
39256171 AAATTAAAATTAAATAAAATCTGTTCCAAGATTTATTCCTGCCGTTTAACAAGATTTTATTTGAT
1 -AATT-AAATTAAATAAAATCTGTTTCAAGATTTATTCCCGCCGTTTAACAAGATTTTATTTGAT
*
39256236 TTTATTTTGTTTCTAAATTAG
64 TTTATTTTGTTTCCAAATTAG
* * ** *
39256257 AATTAAATTAAATTAAATCTGTTTCAAGATATATTCTTGTCGTTTAACAAGATTTTATTTGATTT
1 AATTAAATTAAATAAAATCTGTTTCAAGATTTATTCCCGCCGTTTAACAAGATTTTATTTGATTT
39256322 TATTTTGTTTCCAAATTAG
66 TATTTTGTTTCCAAATTAG
** * * *
39256341 AA-TAAATTAAATAAAATCTGTTTTGAGATTTATCCCCACCGTTTAACAAGATTTTATTTTATTT
1 AATTAAATTAAATAAAATCTGTTTCAAGATTTATTCCCGCCGTTTAACAAGATTTTATTTGATTT
* * *
39256405 AATTTTATTTCTAAATTAG
66 TATTTTGTTTCCAAATTAG
* * * *
39256424 AATTAAATTAAATAAAATATGTTTCAAGA-TT-TTCCCTCCGTTTAACAAGATTTTATTCGATAT
1 AATTAAATTAAATAAAATCTGTTTCAAGATTTATTCCCGCCGTTTAACAAGATTTTATTTGATTT
* ** *
39256487 TGTTTTGTTTCCAAACAAA
66 TATTTTGTTTCCAAATTAG
* * * ** * *
39256506 AACGT-AATCAAAT-AATTCTGTTTTGAGATTTATTCCCGTCGTTTAA-TAGATTTTATTTTGAT
1 AA-TTAAATTAAATAAAATCTGTTTCAAGATTTATTCCCGCCGTTTAACAAGATTTTA-TTTGAT
* *
39256568 ATAATTTTGTTTC
64 TTTATTTTGTTTC
39256581 AGGATTTAAT
Statistics
Matches: 629, Mismatches: 105, Indels: 60
0.79 0.13 0.08
Matches are distributed among these distances:
81 11 0.02
82 58 0.09
83 101 0.16
84 104 0.17
85 45 0.07
86 12 0.02
87 65 0.10
88 34 0.05
89 192 0.31
90 2 0.00
91 4 0.01
92 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (84 bp):
AATTAAATTAAATAAAATCTGTTTCAAGATTTATTCCCGCCGTTTAACAAGATTTTATTTGATTT
TATTTTGTTTCCAAATTAG
Found at i:39264472 original size:40 final size:40
Alignment explanation
Indices: 39264424--39264597 Score: 179
Period size: 40 Copynumber: 4.3 Consensus size: 40
39264414 GAATGAATTT
*
39264424 ACATATGTGCCCCTATTTGTACTTCGGTACCCCTGAATGC
1 ACATACGTGCCCCTATTTGTACTTCGGTACCCCTGAATGC
* * * * **
39264464 TCATATGTGCCCTTGTTTGTACTTTAGTACCCCTGAATGC
1 ACATACGTGCCCCTATTTGTACTTCGGTACCCCTGAATGC
* * *
39264504 ACATACATGCCCATGTTTGTACTTCGGTACCCCTGAATGC
1 ACATACGTGCCCCTATTTGTACTTCGGTACCCCTGAATGC
* * * * *
39264544 GCATACGTACCCCTGA-ATGTACTTCGATACACCTGAATGC
1 ACATACGTGCCCCT-ATTTGTACTTCGGTACCCCTGAATGC
* *
39264584 ACTTACATGCCCCT
1 ACATACGTGCCCCT
39264598 GTTTATCCTC
Statistics
Matches: 110, Mismatches: 23, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
40 110 1.00
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.32
Consensus pattern (40 bp):
ACATACGTGCCCCTATTTGTACTTCGGTACCCCTGAATGC
Found at i:39264565 original size:80 final size:80
Alignment explanation
Indices: 39264439--39264601 Score: 220
Period size: 80 Copynumber: 2.0 Consensus size: 80
39264429 TGTGCCCCTA
* * * * ** *
39264439 TTTGTACTTCGGTACCCCTGAATGCTCATATGTGCCCTTGTTTGTACTTTAG-TACCCCTGAATG
1 TTTGTACTTCGGTACCCCTGAATGCGCATACGTACCCCTGAATGTAC-TTAGATACACCTGAATG
39264503 CACATACATGCCCATG
65 CACATACATGCCCATG
*
39264519 TTTGTACTTCGGTACCCCTGAATGCGCATACGTACCCCTGAATGTACTTCGATACACCTGAATGC
1 TTTGTACTTCGGTACCCCTGAATGCGCATACGTACCCCTGAATGTACTTAGATACACCTGAATGC
* *
39264584 ACTTACATGCCCCTG
66 ACATACATGCCCATG
39264599 TTT
1 TTT
39264602 ATCCTCTAGT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 3 0.04
80 69 0.96
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (80 bp):
TTTGTACTTCGGTACCCCTGAATGCGCATACGTACCCCTGAATGTACTTAGATACACCTGAATGC
ACATACATGCCCATG
Found at i:39264598 original size:20 final size:20
Alignment explanation
Indices: 39264491--39264598 Score: 67
Period size: 20 Copynumber: 5.4 Consensus size: 20
39264481 TGTACTTTAG
*
39264491 TACCCCTGAATGCACATACA
1 TACCCCTGAATGCACTTACA
* * ** * *
39264511 TGCCCATGTTTGTACTT-CGG
1 TACCCCTGAATGCACTTAC-A
* * *
39264531 TACCCCTGAATGCGCATACG
1 TACCCCTGAATGCACTTACA
*
39264551 TACCCCTGAATGTACTT-CGA
1 TACCCCTGAATGCACTTAC-A
*
39264571 TACACCTGAATGCACTTACA
1 TACCCCTGAATGCACTTACA
*
39264591 TGCCCCTG
1 TACCCCTG
39264599 TTTATCCTCT
Statistics
Matches: 62, Mismatches: 22, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
19 2 0.03
20 58 0.94
21 2 0.03
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (20 bp):
TACCCCTGAATGCACTTACA
Found at i:39266296 original size:40 final size:40
Alignment explanation
Indices: 39266114--39266336 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
39266104 TCCTCGTTCA
* * * * *
39266114 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
39266153 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
39266193 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
39266233 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
39266273 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
39266313 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
39266337 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:39266345 original size:41 final size:41
Alignment explanation
Indices: 39266268--39266345 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
39266258 TTAGTATCTC
* * *
39266268 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
39266309 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
39266346 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:39271145 original size:25 final size:25
Alignment explanation
Indices: 39271117--39271206 Score: 103
Period size: 25 Copynumber: 3.6 Consensus size: 25
39271107 TCCTGTACAT
* *
39271117 GTATGCTCATACGAGCTGTGAATCA
1 GTATGCTCATACGAGCTATAAATCA
39271142 GTATGCTCACT-CGAGCTATAAATCA
1 GTATGCTCA-TACGAGCTATAAATCA
**
39271167 GTATGCTC-TCACGAGCTATAAATTG
1 GTATGCTCAT-ACGAGCTATAAATCA
*
39271192 GTATGCTCACACGAG
1 GTATGCTCATACGAG
39271207 TTGTGGAGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
23 1 0.02
25 54 0.96
26 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATAAATCA
Found at i:39272105 original size:20 final size:20
Alignment explanation
Indices: 39272080--39272131 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
39272070 AAAGATTATA
39272080 TTAATTTACTTTTAATTTAC
1 TTAATTTACTTTTAATTTAC
* *
39272100 TTAATTTGTCATTT-ATTTAC
1 TTAATTT-ACTTTTAATTTAC
39272120 -TAA-TTACTTTTA
1 TTAATTTACTTTTA
39272132 TAACATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
17 4 0.15
18 2 0.08
19 3 0.12
20 13 0.50
21 4 0.15
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.60
Consensus pattern (20 bp):
TTAATTTACTTTTAATTTAC
Found at i:39274060 original size:16 final size:16
Alignment explanation
Indices: 39274039--39274071 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39274029 TTTTGTTATC
*
39274039 GTATTAACTTAATTTA
1 GTATTAACTGAATTTA
39274055 GTATTAACTGAATTTA
1 GTATTAACTGAATTTA
39274071 G
1 G
39274072 CTAACTCAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (16 bp):
GTATTAACTGAATTTA
Found at i:39278109 original size:40 final size:40
Alignment explanation
Indices: 39278058--39278193 Score: 209
Period size: 40 Copynumber: 3.4 Consensus size: 40
39278048 TATATATGTC
* * *
39278058 CCCCCGTTTGTACTTCGGTACCCTTGAATGCACACACATG
1 CCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACATG
39278098 CCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACATG
1 CCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACATG
* **
39278138 CCCCTGTTTGTACTTCGGTACCCCTGAATGCATATACACA
1 CCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACATG
*
39278178 CCCCTGATTGTACTTC
1 CCCCTGTTTGTACTTC
39278194 AGTCCCTAAC
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 89 1.00
ACGTcount: A:0.20, C:0.34, G:0.16, T:0.30
Consensus pattern (40 bp):
CCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACATG
Found at i:39278123 original size:20 final size:20
Alignment explanation
Indices: 39278098--39278163 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
39278088 CACACACATG
39278098 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
** * * * *
39278118 CCCCTGAATGCACATAC-ATG
1 CCCCTGTTTGTAC-TTCGGTA
39278138 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
39278158 CCCCTG
1 CCCCTG
39278164 AATGCATATA
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.15, C:0.35, G:0.18, T:0.32
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:39278243 original size:78 final size:78
Alignment explanation
Indices: 39278098--39278250 Score: 175
Period size: 78 Copynumber: 1.9 Consensus size: 78
39278088 CACACACATG
* * * ** *
39278098 CCCCTGTTTGTACTTCGGTACCCCTGAATGCACATACATGCCCCTGTTTGTACTTCGGTACCCCT
1 CCCCTGATTGTACTTCAGTA-CCCTGAATGCACATACATGCCCCTGTTTATACCCCGGTAACCCT
39278163 GAATGCATATACACA
65 GAAT-CATATACACA
* * * *
39278178 CCCCTGATTGTACTTCAGT-CCCT-AACTGCACTTATATGCCCTTGTTTATACCCCGGTAACTCT
1 CCCCTGATTGTACTTCAGTACCCTGAA-TGCACATACATGCCCCTGTTTATACCCCGGTAACCCT
39278241 GAATCATATA
65 GAATCATATA
39278251 GTATAGGATT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
77 8 0.13
78 37 0.60
80 17 0.27
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.32
Consensus pattern (78 bp):
CCCCTGATTGTACTTCAGTACCCTGAATGCACATACATGCCCCTGTTTATACCCCGGTAACCCTG
AATCATATACACA
Found at i:39293707 original size:21 final size:21
Alignment explanation
Indices: 39293681--39293745 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
39293671 TGCTATTTTT
39293681 TATATATTATATAATTTATAA
1 TATATATTATATAATTTATAA
*
39293702 TATATA-TAAATTAAATTTATAA
1 TATATATTATA-T-AATTTATAA
* *
39293724 TAGTATATAATATTA-TTATAA
1 TA-TATATTATATAATTTATAA
39293745 T
1 T
39293746 GTAAACATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
20 3 0.08
21 14 0.39
22 12 0.33
23 5 0.14
24 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TATATATTATATAATTTATAA
Found at i:39293721 original size:22 final size:24
Alignment explanation
Indices: 39293693--39293738 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
39293683 TATATTATAT
39293693 AATTTATAATA-TATATAA-ATTA
1 AATTTATAATAGTATATAATATTA
39293715 AATTTATAATAGTATATAATATTA
1 AATTTATAATAGTATATAATATTA
39293739 TTATAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.50
23 7 0.32
24 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AATTTATAATAGTATATAATATTA
Found at i:39303331 original size:27 final size:27
Alignment explanation
Indices: 39303300--39303356 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
39303290 TATTGGTTCC
39303300 TCAGTATACGTCAAATTAGGCTGAAAT
1 TCAGTATACGTCAAATTAGGCTGAAAT
39303327 TCAGTATACGTCAAATTAGGCTGAAAT
1 TCAGTATACGTCAAATTAGGCTGAAAT
39303354 TCA
1 TCA
39303357 ATCTCACTAT
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:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (27 bp):
TCAGTATACGTCAAATTAGGCTGAAAT
Found at i:39317254 original size:14 final size:14
Alignment explanation
Indices: 39317235--39317264 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39317225 GCCAGTATTC
39317235 TATGTTGGCATAAT
1 TATGTTGGCATAAT
*
39317249 TATGTTGGCTTAAT
1 TATGTTGGCATAAT
39317263 TA
1 TA
39317265 GTCTTCCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (14 bp):
TATGTTGGCATAAT
Found at i:39318026 original size:8 final size:8
Alignment explanation
Indices: 39318013--39318038 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39318003 GACCACAAAA
39318013 ATATTGGG
1 ATATTGGG
39318021 ATATTGGG
1 ATATTGGG
39318029 ATATTGGG
1 ATATTGGG
39318037 AT
1 AT
39318039 TAAGGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (8 bp):
ATATTGGG
Found at i:39321027 original size:21 final size:21
Alignment explanation
Indices: 39321003--39321067 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 21
39320993 GATAGCTCTA
39321003 TTTTACCAGGCAATTGGCTTT
1 TTTTACCAGGCAATTGGCTTT
* *
39321024 TTTTAACC--G---TTAGTTTT
1 TTTT-ACCAGGCAATTGGCTTT
39321041 ATTTTACCAGGCAATTGGCTTT
1 -TTTTACCAGGCAATTGGCTTT
39321063 TTTTA
1 TTTTA
39321068 TCCTGGTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
17 9 0.27
18 4 0.12
19 1 0.03
20 1 0.03
21 9 0.27
22 9 0.27
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.49
Consensus pattern (21 bp):
TTTTACCAGGCAATTGGCTTT
Found at i:39324975 original size:21 final size:20
Alignment explanation
Indices: 39324938--39324991 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
39324928 CGTAGCCTTG
*
39324938 TGTTGAGCCACAACAACCCTA
1 TGTTGAGCCATAACAA-CCTA
* *
39324959 TGTTGAGCCATATCAACCTG
1 TGTTGAGCCATAACAACCTA
*
39324979 TGTTTAGCCATAA
1 TGTTGAGCCATAA
39324992 AGCCTGCATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (20 bp):
TGTTGAGCCATAACAACCTA
Found at i:39324987 original size:20 final size:21
Alignment explanation
Indices: 39324936--39324991 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
39324926 CACGTAGCCT
*
39324936 TGTGTTGAGCCACAACAACCC
1 TGTGTTGAGCCATAACAACCC
* *
39324957 TATGTTGAGCCATATCAA-CC
1 TGTGTTGAGCCATAACAACCC
*
39324977 TGTGTTTAGCCATAA
1 TGTGTTGAGCCATAA
39324992 AGCCTGCATG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTGTTGAGCCATAACAACCC
Found at i:39328954 original size:37 final size:36
Alignment explanation
Indices: 39328869--39328960 Score: 130
Period size: 37 Copynumber: 2.5 Consensus size: 36
39328859 ATTTGGCGTC
*
39328869 TGAGCATTTGGCGTGTTATCGGTTGGATTAGCTCTT
1 TGAGCATTTGGCGTGTTTTCGGTTGGATTAGCTCTT
*
39328905 TGGAGCACTTGGCGTGTTTTCGGTTGGATTAGCTCTT
1 T-GAGCATTTGGCGTGTTTTCGGTTGGATTAGCTCTT
* *
39328942 ATGAGCGTTTGGCATGTTT
1 -TGAGCATTTGGCGTGTTT
39328961 CAGGTGGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
36 1 0.02
37 47 0.96
38 1 0.02
ACGTcount: A:0.13, C:0.14, G:0.32, T:0.41
Consensus pattern (36 bp):
TGAGCATTTGGCGTGTTTTCGGTTGGATTAGCTCTT
Found at i:39330133 original size:19 final size:19
Alignment explanation
Indices: 39330081--39330123 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
39330071 GTGTGTCCCT
39330081 TATTTT-TTGAAAATTTTCA
1 TATTTTCTTG-AAATTTTCA
*
39330100 TATTTTCTTGAAATTTTCT
1 TATTTTCTTGAAATTTTCA
39330119 TATTT
1 TATTT
39330124 GTTTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.63
Consensus pattern (19 bp):
TATTTTCTTGAAATTTTCA
Found at i:39330498 original size:27 final size:26
Alignment explanation
Indices: 39330457--39330606 Score: 96
Period size: 27 Copynumber: 5.6 Consensus size: 26
39330447 CATTTTTCGT
*
39330457 CACAAGGTTTCCTTTATTCA-GATT-GC
1 CACAAGGCTTCCTTTA--CATGATTAGC
*
39330483 CACAAGGGCTTCCTTTACATGGTTAGC
1 CACAA-GGCTTCCTTTACATGATTAGC
*
39330510 CACAAAGGCTTCCTTTACATGGA-TA-A
1 CAC-AAGGCTTCCTTTACAT-GATTAGC
39330536 CATCAAAGGCTTCCTTTACATG-TATAGC
1 CA-C-AAGGCTTCCTTTACATGAT-TAGC
* * *
39330564 CACAAAGGCTCCCATTACAGAGATT-GC
1 CAC-AAGGCTTCCTTTACA-TGATTAGC
*
39330591 CACAAAGGCTTTCTTT
1 CAC-AAGGCTTCCTTT
39330607 TCAAATATGC
Statistics
Matches: 102, Mismatches: 11, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
25 2 0.02
26 11 0.11
27 81 0.79
28 7 0.07
29 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (26 bp):
CACAAGGCTTCCTTTACATGATTAGC
Found at i:39330597 original size:54 final size:53
Alignment explanation
Indices: 39330476--39330769 Score: 199
Period size: 54 Copynumber: 5.4 Consensus size: 53
39330466 TCCTTTATTC
* *
39330476 AGATTGCCACAAGGGCTTCCTTTACATGGT-TAGCCACAAAGGCTTCCTTTACATG
1 AGATTGCCACAAAGGCTTCCTTTACAT-GTAT-GCCACAAAGGCTTCCATTACA-G
** *
39330531 -GA-TAACATCAAAGGCTTCCTTTACATGTATAGCCACAAAGGCTCCCATTACAG
1 AGATTGCCA-CAAAGGCTTCCTTTACATGTAT-GCCACAAAGGCTTCCATTACAG
* * ** * * *
39330584 AGATTGCCACAAAGGCTTTCTTTTCAAATATGCCACAAAGGTTTTCATTTC--
1 AGATTGCCACAAAGGCTTCCTTTACATGTATGCCACAAAGGCTTCCATTACAG
* * * * *
39330635 ATATGTGCCACAAAGGCTTCCATTT-TAGGTATGCCACAAAGGATTCCATTTCAG
1 AGAT-TGCCACAAAGGCTTCC-TTTACATGTATGCCACAAAGGCTTCCATTACAG
* * * * *
39330689 ATATTCGCCACAAAGGCTTTCCTTTCAGAGGTCTGCCATAAAGGCATTCC-TCT-CAG
1 AGATT-GCCACAAAGGC-TTCCTTT-ACATGTATGCCACAAAGGC-TTCCAT-TACAG
*
39330745 AGGTTTGCCACAAAGGCTTTCCTTT
1 A-GATTGCCACAAAGGC-TTCCTTT
39330770 TCTGGTGTTT
Statistics
Matches: 196, Mismatches: 28, Indels: 29
0.77 0.11 0.11
Matches are distributed among these distances:
51 3 0.02
52 37 0.19
53 26 0.13
54 78 0.40
55 7 0.04
56 38 0.19
57 7 0.04
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (53 bp):
AGATTGCCACAAAGGCTTCCTTTACATGTATGCCACAAAGGCTTCCATTACAG
Found at i:39330624 original size:26 final size:26
Alignment explanation
Indices: 39330562--39330765 Score: 156
Period size: 26 Copynumber: 7.6 Consensus size: 26
39330552 TACATGTATA
** * *
39330562 GCCACAAAGGCTCCCATTACAGAGATT
1 GCCACAAAGGCTTTCATTTCAGATA-T
* *
39330589 GCCACAAAGGCTTTCTTTTCAAATAT
1 GCCACAAAGGCTTTCATTTCAGATAT
* * *
39330615 GCCACAAAGGTTTTCATTTCATATGT
1 GCCACAAAGGCTTTCATTTCAGATAT
* * *
39330641 GCCACAAAGGCTTCCATTTTAGGTAT
1 GCCACAAAGGCTTTCATTTCAGATAT
* *
39330667 GCCACAAAGGATTCCATTTCAGATATT
1 GCCACAAAGGCTTTCATTTCAGATA-T
* *
39330694 CGCCACAAAGGCTTTCCTTTCAGAGGTCT
1 -GCCACAAAGGCTTTCATTTCAGA--TAT
* * * * *
39330723 GCCATAAAGGCATTCCTCTCAGAGGTTT
1 GCCACAAAGGCTTTCATTTCAGA--TAT
39330751 GCCACAAAGGCTTTC
1 GCCACAAAGGCTTTC
39330766 CTTTTCTGGT
Statistics
Matches: 144, Mismatches: 29, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
26 65 0.45
27 20 0.14
28 57 0.40
29 1 0.01
30 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (26 bp):
GCCACAAAGGCTTTCATTTCAGATAT
Found at i:39330649 original size:52 final size:52
Alignment explanation
Indices: 39330539--39330715 Score: 160
Period size: 52 Copynumber: 3.3 Consensus size: 52
39330529 TGGATAACAT
* * ** * * * *
39330539 CAAAGGCTTCCTTTACATGTATAGCCACAAAGGCTCCCATTACAGAGATTGCCA
1 CAAAGGCTTTCTTTTCAAATAT-GCCACAAAGGATTCCATTTCA-ATATTGCCA
* *
39330593 CAAAGGCTTTCTTTTCAAATATGCCACAAAGGTTTTCATTTC-ATATGTGCCA
1 CAAAGGCTTTCTTTTCAAATATGCCACAAAGGATTCCATTTCAATAT-TGCCA
* **
39330645 CAAAGGCTTCCATTTT-AGGTATGCCACAAAGGATTCCATTTCAGATATTCGCCA
1 CAAAGGCTTTC-TTTTCAAATATGCCACAAAGGATTCCATTTCA-ATATT-GCCA
*
39330699 CAAAGGCTTTCCTTTCA
1 CAAAGGCTTTCTTTTCA
39330716 GAGGTCTGCC
Statistics
Matches: 101, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
51 3 0.03
52 37 0.37
53 24 0.24
54 37 0.37
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (52 bp):
CAAAGGCTTTCTTTTCAAATATGCCACAAAGGATTCCATTTCAATATTGCCA
Found at i:39333263 original size:17 final size:17
Alignment explanation
Indices: 39333241--39333274 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39333231 TATCAGTTGC
*
39333241 TATTTCAATAGCATTTT
1 TATTTCAATAACATTTT
39333258 TATTTCAATAACATTTT
1 TATTTCAATAACATTTT
39333275 CCATTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTCAATAACATTTT
Found at i:39333282 original size:18 final size:17
Alignment explanation
Indices: 39333242--39333283 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
39333232 ATCAGTTGCT
* *
39333242 ATTTCAATAGCATTTTT
1 ATTTCAATAACATTTTC
39333259 ATTTCAATAACATTTTCC
1 ATTTCAATAACATTTT-C
39333277 ATTTCAA
1 ATTTCAA
39333284 AATCAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (17 bp):
ATTTCAATAACATTTTC
Found at i:39334733 original size:35 final size:34
Alignment explanation
Indices: 39334692--39334791 Score: 119
Period size: 35 Copynumber: 2.9 Consensus size: 34
39334682 AATGCGACGT
* *
39334692 TTAAAAGGTTGGGATAGATAGGTTCTAAGGCAACC
1 TTAAAAGGTTAGGATAGACAGG-TCTAAGGCAACC
* **
39334727 TTAAAAGGGTTAGAATAGACCTGTCTAAGGCAACC
1 TTAAAA-GGTTAGGATAGACAGGTCTAAGGCAACC
*
39334762 TTCAAAAGGTTAGGATAGACACGTCTAAGG
1 TT-AAAAGGTTAGGATAGACAGGTCTAAGG
39334792 TAATTTTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 40 0.73
36 15 0.27
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (34 bp):
TTAAAAGGTTAGGATAGACAGGTCTAAGGCAACC
Found at i:39334736 original size:114 final size:113
Alignment explanation
Indices: 39334532--39334755 Score: 353
Period size: 114 Copynumber: 2.0 Consensus size: 113
39334522 AAGCATACAT
*
39334532 ATGCCGACCTTTAAAGAGTTGGGTCATGCCCACATCAAATGCGACGTTAAAAGGTTGGGATAGAC
1 ATGCCGACCTTTAAAGAGTTGGATCATGCCCACATCAAATGCGACGTTAAAAGGTTGGGATAGAC
39334597 AGGTTCTAAAGCAACCTTAAAAGGGTT-GAGATAGA-CTCGTCTAAGTCC
66 AGGTTCTAAAGCAACCTTAAAAGGGTTAGA-ATAGACCT-GTCTAAGTCC
* **
39334645 ATGCTGACCTTTAAAGAGTTGGATCATGCCCATGTCAAATGCGACGTTTAAAAGGTTGGGATAGA
1 ATGCCGACCTTTAAAGAGTTGGATCATGCCCACATCAAATGCGACG-TTAAAAGGTTGGGATAGA
* *
39334710 TAGGTTCTAAGGCAACCTTAAAAGGGTTAGAATAGACCTGTCTAAG
65 CAGGTTCTAAAGCAACCTTAAAAGGGTTAGAATAGACCTGTCTAAG
39334756 GCAACCTTCA
Statistics
Matches: 102, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
113 42 0.41
114 56 0.55
115 4 0.04
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (113 bp):
ATGCCGACCTTTAAAGAGTTGGATCATGCCCACATCAAATGCGACGTTAAAAGGTTGGGATAGAC
AGGTTCTAAAGCAACCTTAAAAGGGTTAGAATAGACCTGTCTAAGTCC
Found at i:39335637 original size:39 final size:39
Alignment explanation
Indices: 39335588--39335665 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
39335578 ACCAAACTTG
* *
39335588 AATATTCTAACAACTTACGACTACTAAATCCAAAGATAA
1 AATATACTAACAACTTACAACTACTAAATCCAAAGATAA
39335627 AATATACTAACAACTTACAACTACTAAATCCAAAGATAA
1 AATATACTAACAACTTACAACTACTAAATCCAAAGATAA
39335666 CTATTCTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.24
Consensus pattern (39 bp):
AATATACTAACAACTTACAACTACTAAATCCAAAGATAA
Found at i:39342621 original size:12 final size:12
Alignment explanation
Indices: 39342604--39342628 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39342594 GTCCGTACTG
39342604 AACTTAAATTTT
1 AACTTAAATTTT
39342616 AACTTAAATTTT
1 AACTTAAATTTT
39342628 A
1 A
39342629 GTTACAACAG
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
AACTTAAATTTT
Found at i:39342898 original size:21 final size:20
Alignment explanation
Indices: 39342860--39342898 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
39342850 TGTTGGTGAT
*
39342860 CATTTGGTCATGTTTTGTGC
1 CATTTGGTCATGTCTTGTGC
*
39342880 CATTTGAGTTATGTCTTGT
1 CATTTG-GTCATGTCTTGT
39342899 TTTGGATGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.51
Consensus pattern (20 bp):
CATTTGGTCATGTCTTGTGC
Found at i:39344507 original size:59 final size:59
Alignment explanation
Indices: 39344436--39344553 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
39344426 TAGGGTGACC
39344436 GTGTAGGAATCTAAACTTAGCCCCTAAAACAAGCCAATTCAATACCTATCCTTTCCCAA
1 GTGTAGGAATCTAAACTTAGCCCCTAAAACAAGCCAATTCAATACCTATCCTTTCCCAA
*
39344495 GTGTAGGGATCTAAACTTAGCCCCTAAAACAAGCCAATTCAATACCTATCCTTTCCCAA
1 GTGTAGGAATCTAAACTTAGCCCCTAAAACAAGCCAATTCAATACCTATCCTTTCCCAA
39344554 CAAGATAGAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.35, C:0.29, G:0.11, T:0.25
Consensus pattern (59 bp):
GTGTAGGAATCTAAACTTAGCCCCTAAAACAAGCCAATTCAATACCTATCCTTTCCCAA
Found at i:39356342 original size:48 final size:48
Alignment explanation
Indices: 39356271--39356367 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
39356261 TACCTTCAAA
*
39356271 GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCTATT
1 GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCCATT
*
39356319 GCACACACCACCACTACTATTCAATTTAAATCTAGTTGCCTTTCCATT
1 GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCCATT
39356367 G
1 G
39356368 TTCAATTTGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (48 bp):
GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCCATT
Found at i:39360885 original size:39 final size:39
Alignment explanation
Indices: 39360835--39360948 Score: 122
Period size: 39 Copynumber: 2.9 Consensus size: 39
39360825 ACAATCACAT
* * * *
39360835 AACATTTAAGCAAATATCACAATACTCATATAATTACT-T
1 AACATTCAAGCAAATATCGCAATACTCATATAATCA-TAA
* * * *
39360874 AACGTTCAAGCACATATCGTAATACTCATATGATCATAA
1 AACATTCAAGCAAATATCGCAATACTCATATAATCATAA
* *
39360913 AACATTCAAGCATATATCGCAATACCCATATAATCA
1 AACATTCAAGCAAATATCGCAATACTCATATAATCA
39360949 CATAAATTTA
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
38 1 0.02
39 60 0.98
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (39 bp):
AACATTCAAGCAAATATCGCAATACTCATATAATCATAA
Found at i:39363432 original size:20 final size:19
Alignment explanation
Indices: 39363407--39363449 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
39363397 AATACATTTA
* *
39363407 AAAACATGAAAACAAATATT
1 AAAACAAGAAAAAAAATA-T
39363427 AAAACAAGAAAAAAAATAT
1 AAAACAAGAAAAAAAATAT
39363446 AAAA
1 AAAA
39363450 TGATACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAACAAGAAAAAAAATAT
Found at i:39363671 original size:34 final size:34
Alignment explanation
Indices: 39363633--39363704 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
39363623 AAAGAACAAT
* *
39363633 AAAACACCACAAAAAGTA-A-CACCAAAACAACATA
1 AAAACAACACAAAAA-TACAGCACC-AAACAACACA
*
39363667 AAAACAACATAAAAATACAGCACCAAACAACACA
1 AAAACAACACAAAAATACAGCACCAAACAACACA
39363701 AAAA
1 AAAA
39363705 ATAGCATCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 2 0.06
34 27 0.82
35 4 0.12
ACGTcount: A:0.67, C:0.25, G:0.03, T:0.06
Consensus pattern (34 bp):
AAAACAACACAAAAATACAGCACCAAACAACACA
Found at i:39363680 original size:10 final size:11
Alignment explanation
Indices: 39363656--39363681 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39363646 AAGTAACACC
39363656 AAAACAACATA
1 AAAACAACATA
39363667 AAAACAACATA
1 AAAACAACATA
39363678 AAAA
1 AAAA
39363682 TACAGCACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.15, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAACAACATA
Found at i:39366774 original size:16 final size:17
Alignment explanation
Indices: 39366755--39366797 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
39366745 TTTTTATGAT
39366755 TTATATATTTAT-TACC
1 TTATATATTTATGTACC
* *
39366771 TTATATATATATGTACG
1 TTATATATTTATGTACC
39366788 TATATATATT
1 T-TATATATT
39366798 ATACTTTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 4 0.18
18 7 0.32
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (17 bp):
TTATATATTTATGTACC
Found at i:39366782 original size:48 final size:48
Alignment explanation
Indices: 39366728--39366885 Score: 142
Period size: 48 Copynumber: 3.2 Consensus size: 48
39366718 TTTTTAAGTT
*
39366728 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATA
1 TATATATGTAATTATTATTTTTATGATTTATATATTTATTAACTTATA
** * * *
39366776 TATATATGTACGTA-TATATATTAT-ACTTTCTATACATATTT-TATAATTTCTA
1 TATATATGTAATTATTAT-TTTTATGA--TT-TAT--ATATTTAT-TAACTTATA
* * * *
39366828 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATA
1 TATATATGTAATTATTATTTTTATGATTTATATATTTATTAACTTATA
39366876 TATATATGTA
1 TATATATGTA
39366886 CGTATATATG
Statistics
Matches: 84, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
47 4 0.05
48 39 0.46
49 3 0.04
50 6 0.07
51 2 0.02
52 26 0.31
53 4 0.05
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (48 bp):
TATATATGTAATTATTATTTTTATGATTTATATATTTATTAACTTATA
Found at i:39366809 original size:18 final size:18
Alignment explanation
Indices: 39366788--39366839 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
39366778 TATATGTACG
*
39366788 TATATATATTATACTTTC
1 TATATATATTATAATTTC
*
39366806 TATACATATTTTATAATTTC
1 TAT--ATATATTATAATTTC
39366826 TATATATA-TATAAT
1 TATATATATTATAAT
39366840 CATTATCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 6 0.21
18 7 0.24
20 16 0.55
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATATATTATAATTTC
Done.