Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 88 of 170
Found at i:27289586 original size:27 final size:27
Alignment explanation
Indices: 27289556--27289733 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
27289546 ATATTGAGTC
* * * *
27289556 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
27289583 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27289610 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
27289638 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
27289665 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
27289692 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27289719 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
27289734 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:27289695 original size:82 final size:81
Alignment explanation
Indices: 27289577--27289732 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
27289567 TGCTATATAA
* *
27289577 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
27289642 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
27289659 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
27289723 CACTTAGTGC
65 CACTTAGTGC
27289733 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:27291681 original size:42 final size:43
Alignment explanation
Indices: 27291635--27291742 Score: 114
Period size: 44 Copynumber: 2.5 Consensus size: 43
27291625 CCACTGTCCT
* *
27291635 AGACAGGGTCTTACACGAAAT-T-ATATACAATGCCAATATCCC
1 AGACAGGGTCTTACACGAAATCTCAAAT-CAATGCCAACATCCC
* * *
27291677 AGACATGGTCTTACAAGTAAATCTCAAATCGATGCCAACATCCC
1 AGACAGGGTCTTACACG-AAATCTCAAATCAATGCCAACATCCC
*
27291721 AGAC-GAGGTCTTGCACGAAATC
1 AGACAG-GGTCTTACACGAAATC
27291743 ACATATCAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
42 15 0.28
43 9 0.17
44 27 0.50
45 3 0.06
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (43 bp):
AGACAGGGTCTTACACGAAATCTCAAATCAATGCCAACATCCC
Found at i:27297883 original size:3 final size:3
Alignment explanation
Indices: 27297875--27297924 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
27297865 AATTAAAGCT
27297875 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
27297923 AT
1 AT
27297925 GCCTTTGAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:27306721 original size:285 final size:286
Alignment explanation
Indices: 27306347--27306935 Score: 1081
Period size: 285 Copynumber: 2.1 Consensus size: 286
27306337 GCTTCTTTGT
* **
27306347 TCTAAGAAGGTAGCAGGACCGAACAAGGTTTTGTGAAAAAATAACTTTAGTTTCTATATAAACCA
1 TCTAAGAAGGTAGCAGGACCGAACAAGGTCTTGTGAAAAAATAACTGCAGTTTCTATATAAACCA
*
27306412 ACAAAAGTCTCTAAAGGTTAAAGGCAGAAACTTAAAGTATTGACAAAGAGTTGCATTGACAACTG
66 AAAAAAGTCTCTAAAGGTTAAAGGCAGAAACTTAAAGTATTGACAAAGAGTTGCATTGACAACTG
27306477 AATGTCTTCATAAAATACTTGAGAAGACAACAAGTATTCTTAGTTATTTAAGATATTTTCAATCT
131 AATGTCTTCATAAAATACTTGAGAAGACAACAAGTATTCTTAGTTATTTAAGATATTTTCAATCT
*
27306542 AACATCTCTTTTCCAACAGCTCTACCTCAACAACATTTTTTACAACTGTTCTAGGGTCAAATTGG
196 AACAGCTCTTTTCCAACAGCTCTACCTCAACAACATTTTTTACAACTGTTCTAGGGTCAAATTGG
27306607 CTCAAGGCACCAATAAGAAAGTGGAG
261 CTCAAGGCACCAATAAGAAAGTGGAG
*
27306633 TCTAAGAAGGTAGCAGGGCCGAACAAGGTCTT-TGAAAAAATAACTGCAGTTTCTATATAAACCA
1 TCTAAGAAGGTAGCAGGACCGAACAAGGTCTTGTGAAAAAATAACTGCAGTTTCTATATAAACCA
27306697 AAAAAAGTCTCTAAAGGTTAAAGGCAGAAACTTAAAGTATTGACAAAGAGTTGCATTGACAACTG
66 AAAAAAGTCTCTAAAGGTTAAAGGCAGAAACTTAAAGTATTGACAAAGAGTTGCATTGACAACTG
*
27306762 AATGTCTTCATAAAATACTTGAGAAGACAACAAGTATTCTTCGTTATTTAAGATATTTTCAATCT
131 AATGTCTTCATAAAATACTTGAGAAGACAACAAGTATTCTTAGTTATTTAAGATATTTTCAATCT
* *
27306827 AACAGCTCTTTTCCAATAGCTCTACCTCAACAACATTTTTTACAACTGTTCTAGGGTCAAATTTG
196 AACAGCTCTTTTCCAACAGCTCTACCTCAACAACATTTTTTACAACTGTTCTAGGGTCAAATTGG
*
27306892 CTCAAGGCACCAATAAGAAAGTGGTG
261 CTCAAGGCACCAATAAGAAAGTGGAG
27306918 TCTAAGAAGGTAGCAGGA
1 TCTAAGAAGGTAGCAGGA
27306936 AAGTCTCTAA
Statistics
Matches: 292, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
285 262 0.90
286 30 0.10
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (286 bp):
TCTAAGAAGGTAGCAGGACCGAACAAGGTCTTGTGAAAAAATAACTGCAGTTTCTATATAAACCA
AAAAAAGTCTCTAAAGGTTAAAGGCAGAAACTTAAAGTATTGACAAAGAGTTGCATTGACAACTG
AATGTCTTCATAAAATACTTGAGAAGACAACAAGTATTCTTAGTTATTTAAGATATTTTCAATCT
AACAGCTCTTTTCCAACAGCTCTACCTCAACAACATTTTTTACAACTGTTCTAGGGTCAAATTGG
CTCAAGGCACCAATAAGAAAGTGGAG
Found at i:27307111 original size:235 final size:235
Alignment explanation
Indices: 27306700--27307152 Score: 834
Period size: 235 Copynumber: 1.9 Consensus size: 235
27306690 TAAACCAAAA
27306700 AAAGTCTCTAAAGGTTAAAGGCAGAAACTTAAAGTATTGACAAAGAGTTGCATTGACAACTGAAT
1 AAAGTCTCTAAAGGTTAAAGGCAGAAACTTAAAGTATTGACAAAGAGTTGCATTGACAACTGAAT
* *
27306765 GTCTTCATAAAATACTTGAGAAGACAACAAGTATTCTTCGTTATTTAAGATATTTTCAATCTAAC
66 GTCTTCATAAAATACTTGAGAAGACAACAAGTATTCTTAGTTATTTAAGATATTTTCAAGCTAAC
* * * *
27306830 AGCTCTTTTCCAATAGCTCTACCTCAACAACATTTTTTACAACTGTTCTAGGGTCAAATTTGCTC
131 AGCTCTTTTCCAACAACTCTACCTCAACAACATTTTTCACAACTGTTCTAGGGTCAAATTGGCTC
27306895 AAGGCACCAATAAGAAAGTGGTGTCTAAGAAGGTAGCAGG
196 AAGGCACCAATAAGAAAGTGGTGTCTAAGAAGGTAGCAGG
27306935 AAAGTCTCTAAAGGTTAAAGGCAGAAACTTAAAGTATTGACAAAGAGTTGCATTGACAACTGAAT
1 AAAGTCTCTAAAGGTTAAAGGCAGAAACTTAAAGTATTGACAAAGAGTTGCATTGACAACTGAAT
27307000 GTCTTCATAAAATACTTGAGAAGACAACAAGTATTCTTAGTTATTTAAGATATTTTCAAGCTAAC
66 GTCTTCATAAAATACTTGAGAAGACAACAAGTATTCTTAGTTATTTAAGATATTTTCAAGCTAAC
* *
27307065 ATCTCTTTTCCAACAACTCTACCTCAACAATATTTTTCACAACTGTTCTAGGGTCAAATTGGCTC
131 AGCTCTTTTCCAACAACTCTACCTCAACAACATTTTTCACAACTGTTCTAGGGTCAAATTGGCTC
27307130 AAGGCACCAATAAGAAAGTGGTG
196 AAGGCACCAATAAGAAAGTGGTG
27307153 AAACTAACAA
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
235 210 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (235 bp):
AAAGTCTCTAAAGGTTAAAGGCAGAAACTTAAAGTATTGACAAAGAGTTGCATTGACAACTGAAT
GTCTTCATAAAATACTTGAGAAGACAACAAGTATTCTTAGTTATTTAAGATATTTTCAAGCTAAC
AGCTCTTTTCCAACAACTCTACCTCAACAACATTTTTCACAACTGTTCTAGGGTCAAATTGGCTC
AAGGCACCAATAAGAAAGTGGTGTCTAAGAAGGTAGCAGG
Found at i:27317835 original size:31 final size:33
Alignment explanation
Indices: 27317790--27317850 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 33
27317780 TCTACTATTT
* **
27317790 TTTTAAGGTTAGAATAGTTTA-CTCCTAATGTA
1 TTTTAAGGATAGAATAAATTAGCTCCTAATGTA
27317822 TTTT-AGGATAGAATAAATTAGCTCCTAAT
1 TTTTAAGGATAGAATAAATTAGCTCCTAAT
27317851 TCTCATGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (33 bp):
TTTTAAGGATAGAATAAATTAGCTCCTAATGTA
Found at i:27324218 original size:18 final size:19
Alignment explanation
Indices: 27324195--27324232 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
27324185 TAATGATAAG
27324195 ATATG-TGAAATTTAAAAT
1 ATATGTTGAAATTTAAAAT
*
27324213 ATATGTTTAAATTTAAAAT
1 ATATGTTGAAATTTAAAAT
27324232 A
1 A
27324233 CTAAGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
ATATGTTGAAATTTAAAAT
Found at i:27328915 original size:19 final size:19
Alignment explanation
Indices: 27328865--27328911 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
27328855 TTTTTTGAAA
* *
27328865 AAAATTAATTTTAATCAAGT
1 AAAATTAA-ATTAATCAAAT
27328885 AAAATTAAATTAATCAAAT
1 AAAATTAAATTAATCAAAT
27328904 -AAATTAAA
1 AAAATTAAA
27328912 ATTAGTATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATTAAATTAATCAAAT
Found at i:27329341 original size:37 final size:38
Alignment explanation
Indices: 27329290--27329397 Score: 113
Period size: 37 Copynumber: 2.9 Consensus size: 38
27329280 ATTCCAAAAA
*
27329290 AAATATTATTTTAATAGTTTAATATTAAATTTAAT-TT
1 AAATATTATCTTAATAGTTTAATATTAAATTTAATATT
*
27329327 -AATACTTATCTTAATAGTATT-TTATT-AATTTAATATT
1 AAATA-TTATCTTAATAGT-TTAATATTAAATTTAATATT
27329364 AAAGTAATTATCTTAATA--TTAA-ATTAAATTTAAT
1 AAA-T-ATTATCTTAATAGTTTAATATTAAATTTAAT
27329398 GTTTATCTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
36 17 0.28
37 26 0.43
38 4 0.07
39 12 0.20
40 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (38 bp):
AAATATTATCTTAATAGTTTAATATTAAATTTAATATT
Found at i:27329492 original size:59 final size:62
Alignment explanation
Indices: 27329376--27329492 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 62
27329366 AGTAATTATC
* * * *
27329376 TTAATATTAAATTAAATTTAATGTTTATCTTGTAGATAAACATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTAAATCTAATATTTATCTTGTAGATAAACATTATATTAATTTAATAAGAT
* * *
27329438 TTAATATTATATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATA
1 TTAATATTAAATTAAATCTAATATTTATCTTGTAGATAAACATTATATTAATTTAATA
27329493 TTAAAGTGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 21 0.44
60 1 0.02
61 1 0.02
62 25 0.52
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (62 bp):
TTAATATTAAATTAAATCTAATATTTATCTTGTAGATAAACATTATATTAATTTAATAAGAT
Found at i:27346540 original size:20 final size:20
Alignment explanation
Indices: 27346495--27346541 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
27346485 CATATATCAT
*
27346495 TTGCTT-CTTCTTTACTTAG
1 TTGCTTACTTCTTTACTTAC
*
27346514 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTCTTTACTTAC
27346534 TTGCTTAC
1 TTGCTTAC
27346542 ATAAATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.13, C:0.23, G:0.09, T:0.55
Consensus pattern (20 bp):
TTGCTTACTTCTTTACTTAC
Found at i:27346811 original size:49 final size:49
Alignment explanation
Indices: 27346758--27346879 Score: 192
Period size: 49 Copynumber: 2.5 Consensus size: 49
27346748 CAAAGCCATG
* *
27346758 TCCCAGACATGGTCTCACATGGGATGTTTCCTGTACTGCCAATG-CTATA
1 TCCCAGATATGGTCTTACATGGGATGTTTCCTGTACTGCCAATGTC-ATA
*
27346807 TCCCAGATATGGTCTTACATTGGATGTTTCCTGTACTGCCAATGTCATA
1 TCCCAGATATGGTCTTACATGGGATGTTTCCTGTACTGCCAATGTCATA
*
27346856 TCCCAGATATGGTTTTACATGGGA
1 TCCCAGATATGGTCTTACATGGGA
27346880 GTTCTCATAT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
49 66 0.99
50 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (49 bp):
TCCCAGATATGGTCTTACATGGGATGTTTCCTGTACTGCCAATGTCATA
Found at i:27354037 original size:20 final size:20
Alignment explanation
Indices: 27354012--27354050 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
27354002 TCGCTTCTTC
27354012 TTTACTTACTCTCTTACTTG
1 TTTACTTACTCTCTTACTTG
*
27354032 TTTACTTACTTTCTTACTT
1 TTTACTTACTCTCTTACTT
27354051 ATAACTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTACTTACTCTCTTACTTG
Found at i:27354374 original size:50 final size:50
Alignment explanation
Indices: 27354299--27354444 Score: 152
Period size: 50 Copynumber: 2.9 Consensus size: 50
27354289 TTTCCTGCAC
* * * * * * **
27354299 TGCCAATTCCATATCCCATATATGGTTTTACATGGGAGTTCTCATATCGG
1 TGCCAACTCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
* * *
27354349 TGCCCA-TGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACT-CCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
*
27354399 TGCCAACTCCATGTCCCAGACATGGTCTTA-TGTGGGACCTCTCATA
1 TGCCAACTCCATGTCCCAGACATGGTCTTACAG-GGGACCTCTCATA
27354445 ACCTCAATAA
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
49 2 0.03
50 77 0.96
51 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAACTCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
Found at i:27359265 original size:44 final size:44
Alignment explanation
Indices: 27359217--27359311 Score: 154
Period size: 44 Copynumber: 2.2 Consensus size: 44
27359207 ATATCTCAAC
*
27359217 GTCCATGTTTATAACATGGAAATTAAGGAAGAATTGACGAAAAA
1 GTCCATGTTTATAACATGGAAATTAAGAAAGAATTGACGAAAAA
* *
27359261 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
1 GTCCATGTTTATAACATGGAAATTAAGAAAGAATTGACGAAAAA
*
27359305 GACCATG
1 GTCCATG
27359312 GTTTGACCAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (44 bp):
GTCCATGTTTATAACATGGAAATTAAGAAAGAATTGACGAAAAA
Found at i:27359393 original size:50 final size:47
Alignment explanation
Indices: 27359332--27359508 Score: 176
Period size: 50 Copynumber: 3.6 Consensus size: 47
27359322 GGTAGTAAGT
* * *
27359332 GTGCCAATGTAAGACCATGTCTGGGACATGGCATTTGTACAGACCGAGGA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATTAGTAC-GA--GATGA
* * *
27359382 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACGAATAGATAA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATTAGTACG---AGATGA
** * * *
27359432 AAGTCAGTGTAAGACCATGTTTGGGACATGGCATTGGCT-CGAGATGA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATTAG-TACGAGATGA
*
27359479 GTGCTAGTGTAAGACCATGTCTGGGACATG
1 GTGCCAGTGTAAGACCATGTCTGGGACATG
27359509 ACATCGGCAC
Statistics
Matches: 104, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
47 30 0.29
49 1 0.01
50 72 0.69
52 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (47 bp):
GTGCCAGTGTAAGACCATGTCTGGGACATGGCATTAGTACGAGATGA
Found at i:27362169 original size:25 final size:25
Alignment explanation
Indices: 27362141--27362192 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
27362131 ATATGCTTTA
* *
27362141 GATTTATACTTGAATAGGGGATAGT
1 GATTTACAATTGAATAGGGGATAGT
*
27362166 GATTTCCAATTGAATAGGGGATAGT
1 GATTTACAATTGAATAGGGGATAGT
27362191 GA
1 GA
27362193 AATTCCCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.33
Consensus pattern (25 bp):
GATTTACAATTGAATAGGGGATAGT
Found at i:27362203 original size:25 final size:25
Alignment explanation
Indices: 27362148--27362203 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
27362138 TTAGATTTAT
*
27362148 ACTTGAATAGGGGATAGTGATTTCC
1 ACTTGAATAGGGGATAGTGAATTCC
*
27362173 AATTGAATAGGGGATAGTGAAATTCC
1 ACTTGAATAGGGGATAGTG-AATTCC
27362199 -CTTGA
1 ACTTGA
27362204 TCCTTCAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (25 bp):
ACTTGAATAGGGGATAGTGAATTCC
Found at i:27365392 original size:42 final size:42
Alignment explanation
Indices: 27365345--27365424 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
27365335 TAAATCCAAC
* * *
27365345 AACCCATGTTTATCTTCTCCTCTTTTAAATTCTTTTTTCAAA
1 AACCCAAGATTATCTTCTCCTCTTTTAAATTATTTTTTCAAA
*
27365387 AACCCAAGATTATCTTCTCCTTTTTTAAATTATTTTTT
1 AACCCAAGATTATCTTCTCCTCTTTTAAATTATTTTTT
27365425 TCTAAGATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.25, C:0.21, G:0.03, T:0.51
Consensus pattern (42 bp):
AACCCAAGATTATCTTCTCCTCTTTTAAATTATTTTTTCAAA
Found at i:27373142 original size:12 final size:12
Alignment explanation
Indices: 27373125--27373154 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
27373115 GAAATTGCTG
*
27373125 ACAATAATAACA
1 ACAATAACAACA
27373137 ACAATAACAACA
1 ACAATAACAACA
27373149 ACAATA
1 ACAATA
27373155 GATGCAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.67, C:0.20, G:0.00, T:0.13
Consensus pattern (12 bp):
ACAATAACAACA
Found at i:27374106 original size:57 final size:57
Alignment explanation
Indices: 27374014--27374124 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
27374004 ACACGTATAA
*
27374014 AGGAGACAAACAACTCTTCCATTATATCAATAATCCCGCTGAGGATATAAACTATGG
1 AGGAGACAAACAACTCTTCCATTATATCAAGAATCCCGCTGAGGATATAAACTATGG
* * * *
27374071 AGGAGACAAGCAACTCTTCCATTATATCAAGAATCCTGTTGAGGTTATAAACTA
1 AGGAGACAAACAACTCTTCCATTATATCAAGAATCCCGCTGAGGATATAAACTA
27374125 CATCGAGAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (57 bp):
AGGAGACAAACAACTCTTCCATTATATCAAGAATCCCGCTGAGGATATAAACTATGG
Found at i:27385641 original size:40 final size:40
Alignment explanation
Indices: 27385596--27385843 Score: 286
Period size: 40 Copynumber: 6.2 Consensus size: 40
27385586 CGGAATTTAG
* * *
27385596 CCGGATATAACCACAAGCGCAAATGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAAC
* * *
27385636 CCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAAC
* *
27385676 CCGGATAAAATC-ACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CAACTAGCACAAATGCCTTCGGGTCTTAAC
* * * *
27385716 CCGGGTATAGCAATTCA-CACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACT-AGCACAAATGCCTTCGGGTCTTAAC
* *
27385756 CCGGATAAAATC-ACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CAACTAGCACAAATGCCTTCGGGTCTTAAC
* * * *
27385796 CCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAAC
27385836 CCGGATAT
1 CCGGATAT
27385844 CATTCAAATG
Statistics
Matches: 172, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.02
40 166 0.97
41 3 0.02
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:27385715 original size:80 final size:80
Alignment explanation
Indices: 27385592--27385842 Score: 414
Period size: 80 Copynumber: 3.1 Consensus size: 80
27385582 TCTTCGGAAT
* * * * * * *
27385592 TTAG-CCGGATATAACCACAAGCGCAAATGCCTTCGGGTCTTAACCCGGATATATCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
27385656 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* *
27385671 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAATTCACAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
27385736 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
27385751 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
27385816 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
27385831 TTAGCCCGGATA
1 TTAGCCCGGATA
27385843 TCATTCAAAT
Statistics
Matches: 160, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 4 0.03
80 156 0.98
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
AAATGCCTTCGGGTC
Found at i:27385828 original size:120 final size:120
Alignment explanation
Indices: 27385615--27385839 Score: 319
Period size: 120 Copynumber: 1.9 Consensus size: 120
27385605 ACCACAAGCG
* * *
27385615 CAAATGCCTTCGGGTCTTAACCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGG
1 CAAATGCCTTCGGGTCTTAACCCGGATAAATCAACTAGCACAAATGCCTTCGGGTCTTAACCCGG
* *
27385680 ATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAATTCACA
66 ATAAAAGCACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAATTCACA
* *
27385735 CAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAGCACAATTGCCTTCGGGTCTTAACCCG
1 CAAATGCCTTCGGGTCTTAACCCGGAT-AAATCAACTAGCACAAATGCCTTCGGGTCTTAACCCG
* * * *
27385799 GGT-ATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGG
65 GATAAAAGC-ACTAGCACAAATGCCTTCGGGTCTTAACCCGG
27385840 ATATCATTCA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
119 3 0.03
120 85 0.92
121 4 0.04
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGTCTTAACCCGGATAAATCAACTAGCACAAATGCCTTCGGGTCTTAACCCGG
ATAAAAGCACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAATTCACA
Found at i:27393018 original size:37 final size:37
Alignment explanation
Indices: 27392967--27393053 Score: 113
Period size: 37 Copynumber: 2.3 Consensus size: 37
27392957 AAAAAATAGT
27392967 ATAATAGGCATGATTAAAACATGCAATCAGT-AGCAAAA
1 ATAAT-GGCATGATTAAAACATGCAATCAGTGA-CAAAA
* **
27393005 ATAATGGCATGATTCAAACATGTGATCAGTGACAAAA
1 ATAATGGCATGATTAAAACATGCAATCAGTGACAAAA
*
27393042 ATAGTGGCATGA
1 ATAATGGCATGA
27393054 ATTATAATGC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
37 38 0.86
38 6 0.14
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.23
Consensus pattern (37 bp):
ATAATGGCATGATTAAAACATGCAATCAGTGACAAAA
Found at i:27393234 original size:40 final size:40
Alignment explanation
Indices: 27393184--27393294 Score: 168
Period size: 40 Copynumber: 2.8 Consensus size: 40
27393174 TAACGTTACT
* * *
27393184 AGTCACAATTACAGATTAGTGGCTTATTTATAACATAATC
1 AGTCTCAATTACAGATCAGTGGCTTATTTATAACATAAAC
* *
27393224 AGTCTTAATTACAAATCAGTGGCTTATTTATAACATAAAC
1 AGTCTCAATTACAGATCAGTGGCTTATTTATAACATAAAC
27393264 AGTCTCAATTACAGATCAGTGGCTTACTTTA
1 AGTCTCAATTACAGATCAGTGGCTTA-TTTA
27393295 ATATCACAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 59 0.94
41 4 0.06
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (40 bp):
AGTCTCAATTACAGATCAGTGGCTTATTTATAACATAAAC
Found at i:27398671 original size:40 final size:40
Alignment explanation
Indices: 27398627--27398809 Score: 209
Period size: 40 Copynumber: 4.6 Consensus size: 40
27398617 GCTACTCGTT
*
27398627 CAAATGCCTTCGGGACATAGCCCGG-TTATCGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAT-GTAACTCGCA
*
27398667 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAT-GTAACTCGCA
*
27398707 CAAATGCCTTCGGG-CTTAGCCCGGAATTA-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTATGTAACTCGCA
* * *
27398746 CAAATGCCTTC-GGATCTTAGTCCGGA-TATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTAT-GTAAC-TCGCA
27398787 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
27398810 AACATCATTC
Statistics
Matches: 124, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
38 4 0.03
39 30 0.24
40 77 0.62
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATGTAACTCGCA
Found at i:27398744 original size:79 final size:80
Alignment explanation
Indices: 27398627--27398809 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 80
27398617 GCTACTCGTT
*
27398627 CAAATGCCTTCGGGACATAGCCCGGTTATCGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-CGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
27398691 GATTTAGTAAC-TCGCA
64 GATATAGTAACTTAGCA
* **
27398707 CAAATGCCTTCGGG-CTTAGCCCGGAATTA-GTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGG--TTACGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
27398770 GATATGGTCACTTAGCA
64 GATATAGTAACTTAGCA
27398787 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
27398810 AACATCATTC
Statistics
Matches: 90, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
78 3 0.03
79 53 0.59
80 31 0.34
81 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTACGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:27400271 original size:20 final size:20
Alignment explanation
Indices: 27400248--27400329 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 20
27400238 TTATCTACAT
* *
27400248 TATTGGTGGCTTGTCCATAA
1 TATTGGTAGCTTGTCCACAA
*
27400268 TATTGGTAGCTTGTCGACAA
1 TATTGGTAGCTTGTCCACAA
* * * *
27400288 TATTGGCAGTTTATCTA-AA
1 TATTGGTAGCTTGTCCACAA
* *
27400307 TTACTGGTGGCTTGTCCACAA
1 -TATTGGTAGCTTGTCCACAA
27400328 TA
1 TA
27400330 CTAACAACTT
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
19 2 0.04
20 43 0.91
21 2 0.04
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (20 bp):
TATTGGTAGCTTGTCCACAA
Found at i:27400341 original size:60 final size:60
Alignment explanation
Indices: 27400236--27400391 Score: 190
Period size: 60 Copynumber: 2.6 Consensus size: 60
27400226 AGTACTGGTT
* * * * *** * *
27400236 GTTTATCTACATTATTGGTGGCTTGTCCATAATATTGGTAGCTTGTCGACAATATTGGCA
1 GTTTATCTAAATTACTGGTGGCTTGTCCACAATACTAACAACTTGTCGACAATACTGGCA
*
27400296 GTTTATCTAAATTACTGGTGGCTTGTCCACAATACTAACAACTTGTCTACAATACTGGCA
1 GTTTATCTAAATTACTGGTGGCTTGTCCACAATACTAACAACTTGTCGACAATACTGGCA
*
27400356 GTTTATCTACAA-TACTGGTGGATTGTCCACAA-ACTA
1 GTTTATCTA-AATTACTGGTGGCTTGTCCACAATACTA
27400392 GTGTGTTATT
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
59 4 0.05
60 78 0.93
61 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (60 bp):
GTTTATCTAAATTACTGGTGGCTTGTCCACAATACTAACAACTTGTCGACAATACTGGCA
Found at i:27405171 original size:35 final size:34
Alignment explanation
Indices: 27405131--27405229 Score: 126
Period size: 35 Copynumber: 2.9 Consensus size: 34
27405121 ACGATTTAAC
27405131 ATAGTGGCATGCTTAACATGCGAATCAAACTCAGA
1 ATAGTGGCATGCTTAACATGCGAATCAAA-TCAGA
* *
27405166 CTAGTGGCATGCTTAACATGTGAATCATAATCAGA
1 ATAGTGGCATGCTTAACATGCGAATCA-AATCAGA
* * * *
27405201 ATAATAGCACGCTTAACACGCGAATCAAA
1 ATAGTGGCATGCTTAACATGCGAATCAAA
27405230 ATACCAATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.04
35 51 0.93
36 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (34 bp):
ATAGTGGCATGCTTAACATGCGAATCAAATCAGA
Found at i:27415693 original size:25 final size:25
Alignment explanation
Indices: 27415633--27415693 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
27415623 CTCCTAAATT
*
27415633 TTAATTTAATTATCTAATTTTTCAA
1 TTAATTAAATTATCTAATTTTTCAA
* *
27415658 TTTATTGAATTAT-TAATATTTT-ATA
1 TTAATTAAATTATCTAAT-TTTTCA-A
27415683 TTAATTAAATT
1 TTAATTAAATT
27415694 TTTGAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATTTTTCAA
Found at i:27423656 original size:12 final size:13
Alignment explanation
Indices: 27423639--27423672 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
27423629 ATGCAATGGC
27423639 AATTACGAGAAT-
1 AATTACGAGAATA
*
27423651 AATTACGTGAATA
1 AATTACGAGAATA
27423664 AATTACGAG
1 AATTACGAG
27423673 CGAATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (13 bp):
AATTACGAGAATA
Found at i:27449313 original size:46 final size:46
Alignment explanation
Indices: 27449246--27449338 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
27449236 GATTTTTTGA
27449246 AAGACTATGATTGTGCGATCAAGTATCAGCACGAAAAGACTAATGT
1 AAGACTATGATTGTGCGATCAAGTATCAGCACGAAAAGACTAATGT
27449292 AAGACTATGATTGTGCGATCAAGTATCAGCACGAAAAGACTAATGT
1 AAGACTATGATTGTGCGATCAAGTATCAGCACGAAAAGACTAATGT
27449338 A
1 A
27449339 GTGGTCGATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.24
Consensus pattern (46 bp):
AAGACTATGATTGTGCGATCAAGTATCAGCACGAAAAGACTAATGT
Found at i:27451300 original size:50 final size:49
Alignment explanation
Indices: 27451183--27451358 Score: 213
Period size: 50 Copynumber: 3.7 Consensus size: 49
27451173 AAGTGGAGAT
* * *
27451183 TTATCTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTT-TCAGTGGAAG
1 TTATCTGCAAATCAGTGGTGGCTTGTCCATAAAGTATTATCAGTGGTAG
* * * *
27451231 TGTATTTGCATAT--GTGGTGGCCTGTACATAAAGTATTATCAGTGGTAG
1 T-TATCTGCAAATCAGTGGTGGCTTGTCCATAAAGTATTATCAGTGGTAG
27451279 CTTATCTGCAAATCAGTGGTGGCTTGTCCATAAAGTATTATCAGTGGTAG
1 -TTATCTGCAAATCAGTGGTGGCTTGTCCATAAAGTATTATCAGTGGTAG
27451329 TTTATCTGC--A--AGTGGTGGCTTGTCCATAAA
1 -TTATCTGCAAATCAGTGGTGGCTTGTCCATAAA
27451359 TGATACTTTA
Statistics
Matches: 111, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
46 20 0.18
47 20 0.18
48 20 0.18
49 10 0.09
50 41 0.37
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.35
Consensus pattern (49 bp):
TTATCTGCAAATCAGTGGTGGCTTGTCCATAAAGTATTATCAGTGGTAG
Found at i:27453703 original size:15 final size:15
Alignment explanation
Indices: 27453683--27453716 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
27453673 TGGTCCCACT
27453683 ACATATTAAAAATTA
1 ACATATTAAAAATTA
*
27453698 ACATATTAATAATTA
1 ACATATTAAAAATTA
27453713 ACAT
1 ACAT
27453717 GAAAGTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (15 bp):
ACATATTAAAAATTA
Found at i:27462795 original size:25 final size:25
Alignment explanation
Indices: 27462766--27462823 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
27462756 CTGTTTAAAA
*
27462766 ACTGAAAATGCTATAGATAGTA-TAT
1 ACTGAAAATACTATAGATAG-ACTAT
* * *
27462791 ACTGAGACTACTATAGATAGACTGT
1 ACTGAAAATACTATAGATAGACTAT
27462816 ACTGAAAA
1 ACTGAAAA
27462824 CACTCAAGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (25 bp):
ACTGAAAATACTATAGATAGACTAT
Found at i:27465552 original size:17 final size:18
Alignment explanation
Indices: 27465530--27465563 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27465520 TTAAAAAATA
27465530 AAACTTT-ACAAATTGGG
1 AAACTTTGACAAATTGGG
*
27465547 AAACTTTGACAATTTGG
1 AAACTTTGACAAATTGG
27465564 CCTGATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (18 bp):
AAACTTTGACAAATTGGG
Found at i:27473002 original size:36 final size:33
Alignment explanation
Indices: 27472937--27473003 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 33
27472927 GTGAATGAAG
*
27472937 TGAGTGAAAAAGAGAGAGAGCTTAAACAAGGAA
1 TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
* *
27472970 TGAGTGAAGAAGAAGAGAGTGCTCAAACACAAGG
1 TGAGTGAAAAAG-AGAGAGAGCT-AAA-ACAAGG
27473004 GAGGATTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.39
34 9 0.32
35 2 0.07
36 6 0.21
ACGTcount: A:0.48, C:0.09, G:0.31, T:0.12
Consensus pattern (33 bp):
TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
Found at i:27487458 original size:18 final size:18
Alignment explanation
Indices: 27487435--27487470 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
27487425 AAATTAAAAA
27487435 AATCAGA-TCACAAAGAAT
1 AATCAGATTCA-AAAGAAT
27487453 AATCAGATTCAAAAGAAT
1 AATCAGATTCAAAAGAAT
27487471 TCTAGGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.56, C:0.14, G:0.11, T:0.19
Consensus pattern (18 bp):
AATCAGATTCAAAAGAAT
Found at i:27502878 original size:46 final size:46
Alignment explanation
Indices: 27502827--27502920 Score: 172
Period size: 46 Copynumber: 2.0 Consensus size: 46
27502817 ATAGTGTGGC
27502827 GTTCATCATATACCAAGGTTCCTATCA-TCATTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAG
27502873 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
27502919 GT
1 GT
27502921 CTTTTCTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 45 0.96
47 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
Found at i:27504462 original size:22 final size:20
Alignment explanation
Indices: 27504437--27504498 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 20
27504427 AAATGAGATA
27504437 AAAAGAAAAGAGTGAAAAAAAG
1 AAAAGAAAA-A-TGAAAAAAAG
*
27504459 AAAAGAAAAATGAGAAAAAG
1 AAAAGAAAAATGAAAAAAAG
* *
27504479 -AAAGAAAATTTAAAAAAAG
1 AAAAGAAAAATGAAAAAAAG
27504498 A
1 A
27504499 GAGTGAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 9 0.26
21 1 0.03
22 9 0.26
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (20 bp):
AAAAGAAAAATGAAAAAAAG
Found at i:27518381 original size:53 final size:53
Alignment explanation
Indices: 27518301--27518406 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
27518291 AATAAAGAAG
*
27518301 AATGAATAGGAAAAGAATAAAGAAAAGTCCTAAAAAGTCTTGAAATCCCGAAA
1 AATGAACAGGAAAAGAATAAAGAAAAGTCCTAAAAAGTCTTGAAATCCCGAAA
* *
27518354 AATGAACAGGAAAAGAATAAAGAAAAGTCCTAAGAAGTCTTGAAATCCTGAAA
1 AATGAACAGGAAAAGAATAAAGAAAAGTCCTAAAAAGTCTTGAAATCCCGAAA
27518407 GATTCCACAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.17
Consensus pattern (53 bp):
AATGAACAGGAAAAGAATAAAGAAAAGTCCTAAAAAGTCTTGAAATCCCGAAA
Found at i:27528352 original size:29 final size:27
Alignment explanation
Indices: 27528314--27528368 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
27528304 GTGATTAAAT
27528314 AAAATCGACA-CAAGCAAAATTTAAAAGAA
1 AAAATCGACAGCAAG--AAA-TTAAAAGAA
*
27528343 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
27528369 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 3 0.12
29 9 0.38
30 4 0.17
ACGTcount: A:0.62, C:0.11, G:0.13, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:27535075 original size:29 final size:27
Alignment explanation
Indices: 27535037--27535091 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
27535027 ACAAAGTGAT
27535037 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
27535066 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
27535092 TAAGTCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:27536376 original size:21 final size:21
Alignment explanation
Indices: 27536351--27536390 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27536341 CAAATGTGTA
27536351 AGTAAAATTTCAAATCAATTG
1 AGTAAAATTTCAAATCAATTG
* *
27536372 AGTAAAATTTTAGATCAAT
1 AGTAAAATTTCAAATCAAT
27536391 CGGAAAACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (21 bp):
AGTAAAATTTCAAATCAATTG
Found at i:27544978 original size:20 final size:20
Alignment explanation
Indices: 27544944--27544987 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
27544934 GTCTTAACTG
27544944 AATTAATTAGTTCTTAG-TTT
1 AATTAATTAGTTCTT-GTTTT
27544964 AATTAATT-GTGTCTTGTTTT
1 AATTAATTAGT-TCTTGTTTT
27544984 AATT
1 AATT
27544988 TAAGATGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (20 bp):
AATTAATTAGTTCTTGTTTT
Found at i:27546566 original size:21 final size:21
Alignment explanation
Indices: 27546542--27546589 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
27546532 AAAAGGAATT
27546542 GAAAGA-GAGTGAAAAAGAAAA
1 GAAAGATGA-TGAAAAAGAAAA
* **
27546563 GAAAAATGATTCAAAAGAAAA
1 GAAAGATGATGAAAAAGAAAA
27546584 GAAAGA
1 GAAAGA
27546590 AGAGAGATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.67, C:0.02, G:0.23, T:0.08
Consensus pattern (21 bp):
GAAAGATGATGAAAAAGAAAA
Found at i:27547913 original size:13 final size:14
Alignment explanation
Indices: 27547890--27547918 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
27547880 AATAAATTAT
27547890 TTAATTTTAGTTAG
1 TTAATTTTAGTTAG
27547904 TTAA-TTTAGTTAG
1 TTAATTTTAGTTAG
27547917 TT
1 TT
27547919 CAGTTCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TTAATTTTAGTTAG
Found at i:27551359 original size:50 final size:52
Alignment explanation
Indices: 27551283--27551400 Score: 134
Period size: 50 Copynumber: 2.3 Consensus size: 52
27551273 TAATAAAGTT
** *
27551283 ATGCATTATGTAACTTTCATGCTAG-TTAAGTATGCATCA-TAAA-TAATGGC
1 ATGCATTATGTAACTCCCATGCTAGTTTAAGTATACATCATTAAATTAA-GGC
* * *
27551333 ATGCATTATGTAACTCCCATGTTAGTTTAAGTGTACATCATTAAATTAAGTC
1 ATGCATTATGTAACTCCCATGCTAGTTTAAGTATACATCATTAAATTAAGGC
* *
27551385 TTGCATTAAGTAACTC
1 ATGCATTATGTAACTC
27551401 ATTTGTTCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
50 22 0.39
51 12 0.21
52 20 0.35
53 3 0.05
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (52 bp):
ATGCATTATGTAACTCCCATGCTAGTTTAAGTATACATCATTAAATTAAGGC
Found at i:27551815 original size:46 final size:46
Alignment explanation
Indices: 27551743--27551836 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
27551733 GGTTTAAAAG
*
27551743 ACCTTGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
*
27551789 ACCTCGACCCACTATCAAGGATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
27551835 AC
1 AC
27551837 GCCACACTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
Found at i:27554421 original size:20 final size:20
Alignment explanation
Indices: 27554398--27554450 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
27554388 ACTAAGAACG
27554398 AGCTGAATGAGCTAAGGATA
1 AGCTGAATGAGCTAAGGATA
* * * *
27554418 AGCTCAATGAGCTATGGTTG
1 AGCTGAATGAGCTAAGGATA
27554438 AGCTGAATGAGCT
1 AGCTGAATGAGCT
27554451 TGAAGTAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (20 bp):
AGCTGAATGAGCTAAGGATA
Found at i:27560954 original size:20 final size:19
Alignment explanation
Indices: 27560925--27560981 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 19
27560915 AGCTAATAAC
27560925 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
* *
27560944 GAGCTCGAATGAGCTTACTT
1 GAGCTC-AATGAGCTGAATT
27560964 GAGCTCAAGTGAGCTGAA
1 GAGCTCAA-TGAGCTGAA
27560982 CCATATGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 8 0.25
20 24 0.75
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.25
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:27565809 original size:46 final size:46
Alignment explanation
Indices: 27565737--27565830 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
27565727 GGTTTAAAAG
* *
27565737 ACCTTGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGAAACCTTGGTATATGATGA
* *
27565783 ACCTCGACCCACTATCTAGGATGATAGAAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGAAACCTTGGTATATGATGA
27565829 AC
1 AC
27565831 GCCACACTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAATGATAGAAACCTTGGTATATGATGA
Found at i:27578284 original size:40 final size:40
Alignment explanation
Indices: 27578229--27578412 Score: 219
Period size: 40 Copynumber: 4.6 Consensus size: 40
27578219 ATTTGAATGA
*
27578229 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
** *
27578269 TATCCCAGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
27578309 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * *
27578349 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* *
27578389 TACCCGGGTTAAGACCCGAAGGCA
1 TATCCGGGCTAAGACCCGAAGGCA
27578413 ATTGTGCTTG
Statistics
Matches: 132, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 129 0.98
41 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:27578367 original size:80 final size:79
Alignment explanation
Indices: 27578228--27578439 Score: 239
Period size: 80 Copynumber: 2.7 Consensus size: 79
27578218 CATTTGAATG
* * * * *
27578228 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTTTATCCCAGCTAAGTCCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGA-TATAT-CCGGCTAAGACCCGAAGGC
* *
27578292 ATTTATGCTAG-TGATT
64 ATTTATGCGAGTTG-CT
* *
27578308 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATATATCC-GGCTAAGACCCGAAGGCA
*
27578373 TTTGTGCGAGTTGCT
65 TTTATGCGAGTTGCT
* * * * *
27578388 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTTGTTATATCCGGCTAA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATATATCCGGCTAA
27578440 ATTCTGAAGA
Statistics
Matches: 112, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
79 8 0.07
80 99 0.88
81 5 0.04
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATATATCCGGCTAAGACCCGAAGGCAT
TTATGCGAGTTGCT
Found at i:27586540 original size:40 final size:41
Alignment explanation
Indices: 27586388--27586582 Score: 211
Period size: 40 Copynumber: 4.8 Consensus size: 41
27586378 CATTTGAATG
* * *
27586388 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
* * * *
27586428 TTATCCGGGCTAAGTCCCGAAGGGCATTTATAGCGTA-CTGATT
1 ATATCCGGGCTAAGACCCGAA-GGCATTTGT-GCG-AGTTGATT
*
27586471 TTAATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 AT-ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
27586512 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
* * *
27586552 ATACCCGGGTTAAGA-CCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
27586583 TTGTGTATAT
Statistics
Matches: 139, Mismatches: 9, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
39 15 0.11
40 70 0.50
41 12 0.09
42 8 0.06
43 16 0.12
44 18 0.13
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (41 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
Found at i:27588357 original size:39 final size:39
Alignment explanation
Indices: 27588312--27588388 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
27588302 GGATTTAGCA
*
27588312 CGGATAT-ATCAC-TAGCACGAATGCTCTTCGGAACTTAGT
1 CGGATATGATCACTTAGCAC-AAAGC-CTTCGGAACTTAGT
* *
27588351 CGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAG
1 CGGATATGATCACTTAGCACAAAGCCTTCGGAACTTAG
27588389 CCCGGACATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 19 0.58
40 8 0.24
41 6 0.18
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (39 bp):
CGGATATGATCACTTAGCACAAAGCCTTCGGAACTTAGT
Found at i:27588745 original size:29 final size:29
Alignment explanation
Indices: 27588698--27588776 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
27588688 CTTAATAATC
*
27588698 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
27588728 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
27588757 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
27588777 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:27588840 original size:41 final size:42
Alignment explanation
Indices: 27588758--27588858 Score: 186
Period size: 41 Copynumber: 2.4 Consensus size: 42
27588748 TGCATTTCAA
27588758 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCT-ACAACCGTGAACACTTATT
27588801 GCCCGCACACTTAGTGCCAATCT-CAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTACAACCGTGAACACTTATT
27588842 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
27588859 TGAAAACCAA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
41 35 0.60
43 23 0.40
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.23
Consensus pattern (42 bp):
GCCCGCACACTTAGTGCCAATCTACAACCGTGAACACTTATT
Found at i:27590770 original size:38 final size:37
Alignment explanation
Indices: 27590696--27590775 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 37
27590686 TTATTACGAA
* * * *
27590696 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
*
27590733 GTCTTACCCGAACAAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGAAC-AAAATCCCCACACGAAGTCATCGG
27590771 GTCTT
1 GTCTT
27590776 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 12 0.32
38 25 0.68
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
Found at i:27590997 original size:43 final size:46
Alignment explanation
Indices: 27590893--27591066 Score: 205
Period size: 47 Copynumber: 3.8 Consensus size: 46
27590883 GCCTTCGGGA
* * * * * * *
27590893 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
* *
27590940 CCTGTCACATATATACACTTTCACATTCA-ACATC-GCCATTA-GC
1 CTTATCACATATATACACTTTCACATTCACACATCGGCCATTAGGC
27590983 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
27591030 CTTAT-ACATATATACACTTTCACATT-ATCACATCGGC
1 CTTATCACATATATACACTTTCACATTCA-CACATCGGC
27591067 TATATTACAC
Statistics
Matches: 112, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
43 29 0.26
44 5 0.04
45 19 0.17
46 28 0.25
47 31 0.28
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (46 bp):
CTTATCACATATATACACTTTCACATTCACACATCGGCCATTAGGC
Found at i:27591064 original size:90 final size:90
Alignment explanation
Indices: 27590893--27591055 Score: 238
Period size: 90 Copynumber: 1.8 Consensus size: 90
27590883 GCCTTCGGGA
* * * * * *
27590893 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
27590958 TTTCACATTCAACATCGCCATTAGC
66 TTTCACATTCAACATCGCCATTAGC
* * *
27590983 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-ACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
27591047 TTTCACATT
66 TTTCACATT
27591056 ATCACATCGG
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
89 21 0.33
90 43 0.67
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (90 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCAACATCGCCATTAGC
Found at i:27591076 original size:30 final size:31
Alignment explanation
Indices: 27591037--27591099 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
27591027 GGCCTTATAC
27591037 ATATATACACTTTCACATT-ATCACATCGGCT
1 ATATATACACTTTCACATTCATCACATC-GCT
27591068 ATAT-TACACTTTCACATTCATCACATCGCT
1 ATATATACACTTTCACATTCATCACATCGCT
27591098 AT
1 AT
27591100 TAGGCCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (31 bp):
ATATATACACTTTCACATTCATCACATCGCT
Found at i:27591081 original size:76 final size:78
Alignment explanation
Indices: 27590991--27591146 Score: 273
Period size: 76 Copynumber: 2.0 Consensus size: 78
27590981 GCCTTATCAC
27590991 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-ACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATC-GCCATTAGGCCTTATCACATATATACACTTTCACAT
27591055 T-ATCACATCGGCT
65 TCATCACATCGGCT
*
27591068 ATAT-TACACTTTCACATTCATCACATCGCTATTAGGCCTTATCACATATATACACTTTCACATT
1 ATATATACACTTTCACATTCATCACATCGCCATTAGGCCTTATCACATATATACACTTTCACATT
27591132 CATCACATCGGCT
66 CATCACATCGGCT
27591145 AT
1 AT
27591147 TAGGCCTTAT
Statistics
Matches: 76, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
75 14 0.18
76 44 0.58
77 18 0.24
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.35
Consensus pattern (78 bp):
ATATATACACTTTCACATTCATCACATCGCCATTAGGCCTTATCACATATATACACTTTCACATT
CATCACATCGGCT
Found at i:27591118 original size:122 final size:121
Alignment explanation
Indices: 27590948--27591192 Score: 406
Period size: 122 Copynumber: 2.0 Consensus size: 121
27590938 GCCCTGTCAC
27590948 ATATATACACTTTCACATTCAACATCGCCATTAGCCTTATCACATATATACACTTTCACATTCAT
1 ATATATACACTTTCACATTCAACATCGCCATTAGCCTTATCACATATATACACTTTCACATTCAT
27591013 CACATCGGCCATTAGGCCTTAT-ACATATATACACTTTCACATT-ATCACATCGGCT
66 CACATCGGCCATTAGGCCTTATCACATATATACAC-TTCACATTCATCACATCGGCT
*
27591068 ATAT-TACACTTTCACATTCATCACATCGCTATTAGGCCTTATCACATATATACACTTTCACATT
1 ATATATACACTTTCACATTCA--ACATCGCCATTA-GCCTTATCACATATATACACTTTCACATT
* *
27591132 CATCACATCGGCTATTAGGCCTTATCACCTATATACACTTCACATTCATCACATCGGCT
63 CATCACATCGGCCATTAGGCCTTATCACATATATACACTTCACATTCATCACATCGGCT
27591191 AT
1 AT
27591193 TAGGCTTATC
Statistics
Matches: 117, Mismatches: 3, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
119 16 0.14
120 4 0.03
121 11 0.09
122 61 0.52
123 25 0.21
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.34
Consensus pattern (121 bp):
ATATATACACTTTCACATTCAACATCGCCATTAGCCTTATCACATATATACACTTTCACATTCAT
CACATCGGCCATTAGGCCTTATCACATATATACACTTCACATTCATCACATCGGCT
Found at i:27591149 original size:47 final size:47
Alignment explanation
Indices: 27591067--27591281 Score: 330
Period size: 46 Copynumber: 4.6 Consensus size: 47
27591057 TCACATCGGC
27591067 TATATTACACTTTCACATTCATCACATC-GCTATTAGGCCTTATCACA
1 TATA-TACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACA
*
27591114 TATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACC
1 TATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACA
27591161 TATATACAC-TTCACATTCATCACATCGGCTATTAGG-CTTATCACA
1 TATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACA
* *
27591206 CATATACACTTTCACATTCATCACATCGGC-ATTTGGCCCTTATCACA
1 TATATACACTTTCACATTCATCACATCGGCTATTAGG-CCTTATCACA
* *
27591253 CACAATACACTTTCACATTCATCACATCG
1 TA-TATACACTTTCACATTCATCACATCG
27591282 ACCATTTGGC
Statistics
Matches: 158, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
45 21 0.13
46 70 0.44
47 42 0.27
48 25 0.16
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (47 bp):
TATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACA
Found at i:27619774 original size:13 final size:13
Alignment explanation
Indices: 27619752--27619794 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
27619742 AACACAAAAT
27619752 AAATTTTTTTTTC
1 AAATTTTTTTTTC
*
27619765 GGAATTTTTTTTTC
1 -AAATTTTTTTTTC
*
27619779 AAATTTTTTTTAC
1 AAATTTTTTTTTC
27619792 AAA
1 AAA
27619795 CTCGTAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (13 bp):
AAATTTTTTTTTC
Found at i:27621672 original size:36 final size:37
Alignment explanation
Indices: 27621632--27621704 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
27621622 TTCAAAAACC
27621632 TGCAAAACAAACAC-TCAA-CACTCAAAAAGAAAAATT
1 TGCAAAACAAAC-CGTCAATCACTCAAAAAGAAAAATT
* ** *
27621668 TGCAAACCTCACCGTTAATCACTCAAAAAGAAAAATT
1 TGCAAAACAAACCGTCAATCACTCAAAAAGAAAAATT
27621705 AAATTCTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 1 0.03
36 12 0.39
37 18 0.58
ACGTcount: A:0.52, C:0.23, G:0.07, T:0.18
Consensus pattern (37 bp):
TGCAAAACAAACCGTCAATCACTCAAAAAGAAAAATT
Found at i:27630460 original size:6 final size:6
Alignment explanation
Indices: 27630439--27630496 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
27630429 CTTTTTTCGA
* * *
27630439 TTTTC- TTTTC- TTTTCT TTTTCT TTCTCT CTCTT-T TTTTCT TGTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT -TTTTCT TTTTCT TTTTCT
27630485 TTTTCT TTTTCT
1 TTTTCT TTTTCT
27630497 ACAGTCTCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
5 13 0.30
6 29 0.66
7 2 0.05
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:27630505 original size:35 final size:34
Alignment explanation
Indices: 27630439--27630508 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 34
27630429 CTTTTTTCGA
* *
27630439 TTTTCTTTTCTTTTCTTTTTCTTTCTCTCTCTTT
1 TTTTCTTTTCTTTTCTTTTTCTTACACTCTCTTT
*
27630473 TTTTCTTGTTCTTTTTCTTTTTC-TACAGTCTCTTT
1 TTTTCTT-TTC-TTTTCTTTTTCTTACACTCTCTTT
27630508 T
1 T
27630509 AGCTTGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 7 0.23
35 13 0.42
36 11 0.35
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.73
Consensus pattern (34 bp):
TTTTCTTTTCTTTTCTTTTTCTTACACTCTCTTT
Found at i:27638884 original size:9 final size:9
Alignment explanation
Indices: 27638870--27638913 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
27638860 TTTTGTTACA
27638870 ACAATTAAT
1 ACAATTAAT
27638879 ACAATTAAT
1 ACAATTAAT
27638888 ACAATT-A-
1 ACAATTAAT
27638895 ACAATTAAT
1 ACAATTAAT
27638904 ACAATTAAT
1 ACAATTAAT
27638913 A
1 A
27638914 ATTTGATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.18
8 2 0.06
9 25 0.76
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:27638900 original size:16 final size:16
Alignment explanation
Indices: 27638879--27638916 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
27638869 AACAATTAAT
27638879 ACAATTAATACAATTA
1 ACAATTAATACAATTA
27638895 ACAATTAATACAATTA
1 ACAATTAATACAATTA
*
27638911 ATAATT
1 ACAATT
27638917 TGATAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (16 bp):
ACAATTAATACAATTA
Found at i:27639023 original size:66 final size:65
Alignment explanation
Indices: 27638883--27639026 Score: 147
Period size: 66 Copynumber: 2.2 Consensus size: 65
27638873 ATTAATACAA
* * *
27638883 TTAAT-ACAATT-AACAATTAATACAATTAATAATTTGATAATTTTATTAATCAAATCTTAGATT
1 TTAATAACAATTAAACAATTAATACAATTAATAATTTGATAATTTTACTAATCAAAACCTAGATT
*
27638946 TTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGATAATTTTACTAA-CAAGTAACAA
1 TTA--ATAACAATTAA-ACAATTAATACAATTAATAATTTGATAATTTTACTAATCAA--AAC--
27639008 CTA-ATT
59 CTAGATT
27639014 TTAATAACAATTA
1 TTAATAACAATTA
27639027 GTTTTAATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
63 3 0.04
65 4 0.06
66 42 0.63
67 4 0.06
68 12 0.18
69 2 0.03
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.40
Consensus pattern (65 bp):
TTAATAACAATTAAACAATTAATACAATTAATAATTTGATAATTTTACTAATCAAAACCTAGATT
Found at i:27639054 original size:21 final size:22
Alignment explanation
Indices: 27639009--27639061 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
27638999 AAGTAACAAC
* *
27639009 TAATTTTAATAACAATTAGTTT
1 TAATTTTAATAACAAATAATTT
*
27639031 TAATTTTATTAA-AAATAATTT
1 TAATTTTAATAACAAATAATTT
27639052 TAATTTTAAT
1 TAATTTTAAT
27639062 TTTAATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TAATTTTAATAACAAATAATTT
Found at i:27644510 original size:42 final size:42
Alignment explanation
Indices: 27644441--27644523 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
27644431 AAATTCAAAG
* *
27644441 GGATGAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAAAAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
*
27644483 GGATAAGAAAAAGAGTTCAAATGTTTGAATTTCAAATGTTT
1 GGATAAGAAAAAGAGTTCAAATGTTTGAATTTCAAACGTTT
27644524 CACACATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (42 bp):
GGATAAGAAAAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
Found at i:27645179 original size:35 final size:36
Alignment explanation
Indices: 27645131--27645201 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 36
27645121 TTATATATTG
27645131 ATCAAAGTATTTAAAA-AAGCAAA-AAAAAAATTCGAAT
1 ATCAAAG-ATTTAAAAGAA--AAAGAAAAAAATTCGAAT
27645168 ATCAAAG-TTTAAAAGAAAAAGAAAAAAATTCGAA
1 ATCAAAGATTTAAAAGAAAAAGAAAAAAATTCGAA
27645202 CAATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
34 3 0.09
35 20 0.62
36 2 0.06
37 7 0.22
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (36 bp):
ATCAAAGATTTAAAAGAAAAAGAAAAAAATTCGAAT
Found at i:27667511 original size:23 final size:23
Alignment explanation
Indices: 27667480--27667530 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
27667470 ACTTACTTTC
* *
27667480 TTACTGTAGTAATTTTCAGGGTA
1 TTACAGTAGTAATTTTCAGGATA
27667503 TTACAGTAGTAATTTTCAGGATA
1 TTACAGTAGTAATTTTCAGGATA
27667526 TTACA
1 TTACA
27667531 CTTATAGGTC
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:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCAGGATA
Found at i:27669409 original size:20 final size:19
Alignment explanation
Indices: 27669374--27669421 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
27669364 ATGTAATAAT
* *
27669374 CTAAGACAATTTAATTGAA
1 CTAAGACAAATTAATTCAA
*
27669393 CTAAGACAGAATTAATTCAG
1 CTAAGACA-AATTAATTCAA
27669413 CTAAGACAA
1 CTAAGACAA
27669422 GGCGTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (19 bp):
CTAAGACAAATTAATTCAA
Found at i:27673124 original size:38 final size:38
Alignment explanation
Indices: 27673073--27673293 Score: 291
Period size: 38 Copynumber: 5.8 Consensus size: 38
27673063 ACACTGGTAA
* * *
27673073 TAAGCCTACTAGGCACTAAGCTTGAATAACACCGGCAT
1 TAAGCCTGCTAGGCACAAAGCTTGAATAACACCGGCAC
* * *
27673111 TAAGCTTGCTAGGCACAAAGCCTGAATAACATCGAG-AC
1 TAAGCCTGCTAGGCACAAAGCTTGAATAACACCG-GCAC
* * *
27673149 TAAGCCTGTTAGGCACAAAGCCTGAATAACACAGGCAC
1 TAAGCCTGCTAGGCACAAAGCTTGAATAACACCGGCAC
* * * *
27673187 AAAGCCTGCTAGGCACAAAACTTGAATAACACTGGTAC
1 TAAGCCTGCTAGGCACAAAGCTTGAATAACACCGGCAC
*
27673225 TAAGCCTGCTAGGCACAAAGCTTGAATAACACTGGCAC
1 TAAGCCTGCTAGGCACAAAGCTTGAATAACACCGGCAC
*
27673263 TAAGCCTGCTAGGCACAAAGCGTGAATAACA
1 TAAGCCTGCTAGGCACAAAGCTTGAATAACA
27673294 TTATGATTCA
Statistics
Matches: 161, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
37 1 0.01
38 159 0.99
39 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (38 bp):
TAAGCCTGCTAGGCACAAAGCTTGAATAACACCGGCAC
Found at i:27680580 original size:22 final size:21
Alignment explanation
Indices: 27680545--27680587 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
27680535 CATCACATAT
27680545 TATCTTAAAGTTTACGTTTTTC
1 TATCTTAAAGTTTAC-TTTTTC
* *
27680567 TATCTTGAATTTTACTTTTTC
1 TATCTTAAAGTTTACTTTTTC
27680588 AAATGATCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.58
Consensus pattern (21 bp):
TATCTTAAAGTTTACTTTTTC
Found at i:27682067 original size:22 final size:22
Alignment explanation
Indices: 27682039--27682084 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
27682029 AGTTATATAC
27682039 TAAGTGATTCAATTGATTAAGT
1 TAAGTGATTCAATTGATTAAGT
27682061 TAAGTGATTCAATTGATTAAGT
1 TAAGTGATTCAATTGATTAAGT
27682083 TA
1 TA
27682085 TTAAGCATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (22 bp):
TAAGTGATTCAATTGATTAAGT
Found at i:27692880 original size:23 final size:23
Alignment explanation
Indices: 27692830--27692892 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
27692820 AATTTGGTTT
**
27692830 ATTTCGTACCAAAAGTTCCATACA
1 ATTTCGTACCAAAA-CCCCATACA
*
27692854 ATTTCGTACCAAAACCCCATACC
1 ATTTCGTACCAAAACCCCATACA
27692877 ATTTCGTACCAAAACC
1 ATTTCGTACCAAAACC
27692893 AACTCCATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 22 0.61
24 14 0.39
ACGTcount: A:0.37, C:0.32, G:0.06, T:0.25
Consensus pattern (23 bp):
ATTTCGTACCAAAACCCCATACA
Found at i:27693946 original size:12 final size:12
Alignment explanation
Indices: 27693929--27693953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27693919 AAAATCTGAT
27693929 TTCAATGTGTAA
1 TTCAATGTGTAA
27693941 TTCAATGTGTAA
1 TTCAATGTGTAA
27693953 T
1 T
27693954 GTATAAGGGT
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:27695481 original size:39 final size:39
Alignment explanation
Indices: 27695398--27695485 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
27695388 TGAAAATCAA
* * *
27695398 AAAAAGAAAAGAAAATTGAGAGAAAAAGAGGGAAAATTG
1 AAAAAGAAAAGAAAATAGAGAGAAAAAGAGGAAAAACTG
* *
27695437 TAAAAGAAAATGAAAATAGAGTGAAAAA-A-GAAAACACTG
1 AAAAAGAAAA-GAAAATAGAGAGAAAAAGAGGAAAA-ACTG
27695476 AAAAAGAAAA
1 AAAAAGAAAA
27695486 AGAATGTGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
38 4 0.10
39 22 0.54
40 15 0.37
ACGTcount: A:0.67, C:0.02, G:0.20, T:0.10
Consensus pattern (39 bp):
AAAAAGAAAAGAAAATAGAGAGAAAAAGAGGAAAAACTG
Found at i:27697892 original size:26 final size:26
Alignment explanation
Indices: 27697863--27697912 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
27697853 AATTCAGTCG
27697863 AAAAAGCCAAAAAAAATTGAAAAATA
1 AAAAAGCCAAAAAAAATTGAAAAATA
* * *
27697889 AAAAATCCAATAAAAATTTAAAAA
1 AAAAAGCCAAAAAAAATTGAAAAA
27697913 AAGATTTAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.72, C:0.08, G:0.04, T:0.16
Consensus pattern (26 bp):
AAAAAGCCAAAAAAAATTGAAAAATA
Found at i:27700401 original size:18 final size:20
Alignment explanation
Indices: 27700380--27700429 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
27700370 AAAGAAAGAC
27700380 AGAAAAAGA-AATCAAAAA-
1 AGAAAAAGAGAATCAAAAAG
*
27700398 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATCAAAAAG
27700418 AGAAAAAAGAGA
1 AG-AAAAAGAGA
27700430 TTGAGAGTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 2 0.07
21 9 0.32
ACGTcount: A:0.74, C:0.02, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATCAAAAAG
Found at i:27705141 original size:11 final size:12
Alignment explanation
Indices: 27705125--27705153 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
27705115 CCCGAAATTA
27705125 AAAAAATTT-TG
1 AAAAAATTTGTG
27705136 AAAAAATTTGTG
1 AAAAAATTTGTG
27705148 AAAAAA
1 AAAAAA
27705154 ACAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (12 bp):
AAAAAATTTGTG
Found at i:27705181 original size:17 final size:17
Alignment explanation
Indices: 27705159--27705196 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
27705149 AAAAAACAAA
*
27705159 AAAAAATTGTG-TGCTAC
1 AAAAAAGTGTGTTG-TAC
27705176 AAAAAAGTGTGTTGTAC
1 AAAAAAGTGTGTTGTAC
27705193 AAAA
1 AAAA
27705197 TACAAGTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.26
Consensus pattern (17 bp):
AAAAAAGTGTGTTGTAC
Found at i:27706316 original size:17 final size:18
Alignment explanation
Indices: 27706294--27706333 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
27706284 ATGAGATTTC
27706294 AAAAAC-AAAAGAGAGTG
1 AAAAACAAAAAGAGAGTG
*
27706311 AAAAACAAAAAGAGATTG
1 AAAAACAAAAAGAGAGTG
27706329 AAAAA
1 AAAAA
27706334 GAAATTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.70, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAACAAAAAGAGAGTG
Found at i:27706400 original size:16 final size:16
Alignment explanation
Indices: 27706379--27706422 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
27706369 AGATTTTGCA
*
27706379 AAAGAAACGAGTGAAG
1 AAAGAAACAAGTGAAG
27706395 AAAGAAACAAGTGAAG
1 AAAGAAACAAGTGAAG
27706411 AAAGAAAACAAG
1 AAAG-AAACAAG
27706423 AAAAAGTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.64, C:0.07, G:0.25, T:0.05
Consensus pattern (16 bp):
AAAGAAACAAGTGAAG
Found at i:27724767 original size:19 final size:20
Alignment explanation
Indices: 27724743--27724780 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
27724733 TGAGCTGGTT
27724743 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
27724762 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
27724781 AATCAGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:27729710 original size:145 final size:145
Alignment explanation
Indices: 27729447--27729737 Score: 582
Period size: 145 Copynumber: 2.0 Consensus size: 145
27729437 CGAAGCTCTG
27729447 TTGTTGAGTTAACCTTTGTCAAATGGAACTCAAACTTCATGTACAACCACAGAAACTGTTTAAGG
1 TTGTTGAGTTAACCTTTGTCAAATGGAACTCAAACTTCATGTACAACCACAGAAACTGTTTAAGG
27729512 CACGAATATAATTTGAAAAAAAATTTGGCAAATTTCGTTACCTTATTCAAAAACCAAGTATCAAA
66 CACGAATATAATTTGAAAAAAAATTTGGCAAATTTCGTTACCTTATTCAAAAACCAAGTATCAAA
27729577 ACAATAGAAAGTATT
131 ACAATAGAAAGTATT
27729592 TTGTTGAGTTAACCTTTGTCAAATGGAACTCAAACTTCATGTACAACCACAGAAACTGTTTAAGG
1 TTGTTGAGTTAACCTTTGTCAAATGGAACTCAAACTTCATGTACAACCACAGAAACTGTTTAAGG
27729657 CACGAATATAATTTGAAAAAAAATTTGGCAAATTTCGTTACCTTATTCAAAAACCAAGTATCAAA
66 CACGAATATAATTTGAAAAAAAATTTGGCAAATTTCGTTACCTTATTCAAAAACCAAGTATCAAA
27729722 ACAATAGAAAGTATT
131 ACAATAGAAAGTATT
27729737 T
1 T
27729738 GCACACAATA
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 146 1.00
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (145 bp):
TTGTTGAGTTAACCTTTGTCAAATGGAACTCAAACTTCATGTACAACCACAGAAACTGTTTAAGG
CACGAATATAATTTGAAAAAAAATTTGGCAAATTTCGTTACCTTATTCAAAAACCAAGTATCAAA
ACAATAGAAAGTATT
Found at i:27735133 original size:43 final size:43
Alignment explanation
Indices: 27735072--27735159 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
27735062 GGTATGTATG
27735072 TGAAAATCCTCATGGTTTAACGTGATTGGTTTAATGAAATCTT
1 TGAAAATCCTCATGGTTTAACGTGATTGGTTTAATGAAATCTT
27735115 TGAAAATCCTCATGGTTTAACGTGATTGGTTTAATGAAATCTT
1 TGAAAATCCTCATGGTTTAACGTGATTGGTTTAATGAAATCTT
27735158 TG
1 TG
27735160 TTACACTTCG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (43 bp):
TGAAAATCCTCATGGTTTAACGTGATTGGTTTAATGAAATCTT
Found at i:27742416 original size:80 final size:79
Alignment explanation
Indices: 27742271--27742442 Score: 188
Period size: 80 Copynumber: 2.2 Consensus size: 79
27742261 ATGTCTGGGC
* **
27742271 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAACGAG
27742336 TTA-CTAAATCCGGGT
66 -TAGCTAAATCC-GGT
* * * * *
27742351 TAAGTCCCGAAGGCATTTGTG-TGAGTTACTATAACCGGGCTATG-TCCCGAAGGCATTTGAACG
1 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCATTTGAACG
*
27742414 AGTAGCTATATCCGGT
64 AGTAGCTAAATCCGGT
* *
27742430 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
27742443 TATGTGATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
79 17 0.22
80 55 0.71
81 6 0.08
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (79 bp):
TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAACGAG
TAGCTAAATCCGGT
Found at i:27742423 original size:40 final size:40
Alignment explanation
Indices: 27742267--27742409 Score: 166
Period size: 40 Copynumber: 3.6 Consensus size: 40
27742257 AATGATGTCT
* * * *
27742267 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACC
*
27742307 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AATCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
* *
27742347 GGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
*
27742387 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
27742410 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
39 2 0.02
40 76 0.86
41 10 0.11
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
Found at i:27742703 original size:47 final size:47
Alignment explanation
Indices: 27742634--27742801 Score: 255
Period size: 47 Copynumber: 3.6 Consensus size: 47
27742624 AAGGGTTGGT
*
27742634 AATGTGAAAGTGTATATATGTGATAAGGTCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
27742681 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
27742728 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
27742775 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
27742802 TCCCGAAGGG
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 110 1.00
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:27744306 original size:40 final size:40
Alignment explanation
Indices: 27744251--27744639 Score: 534
Period size: 40 Copynumber: 9.8 Consensus size: 40
27744241 GAGAATTGAG
27744251 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
27744291 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * * *
27744331 AGTGATGTATCCGGGCTAAATTCCAAAGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
27744371 AGTGATGTATCCGGGCTAAAT--CGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
27744409 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
27744449 AGTGATGTATCCAGGCTGAA-TTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCT-AAGTCCCGAAGAGCATTCGTGCT
*
27744489 AGTGATATATCCGGGCTAAGT-CCGAAGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
27744528 AGTGATGTATCCGGGCTAAATTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* **
27744568 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
27744608 GGTGTTATGTCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
27744640 ATCATGCTGG
Statistics
Matches: 313, Mismatches: 31, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
38 34 0.11
39 38 0.12
40 239 0.76
41 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:27744471 original size:118 final size:119
Alignment explanation
Indices: 27744251--27744639 Score: 557
Period size: 118 Copynumber: 3.3 Consensus size: 119
27744241 GAGAATTGAG
27744251 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
1 AGTGATATATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
*
27744316 AAGAGCATTCATGCTAGTGATGTATCCGGGCTAAATTCCAAAGAGCATTCATGCT
65 AAGAGCATTCATGCTAGTGATGTATCCAGGCTAAATTCCAAAGAGCATTCATGCT
* *
27744371 AGTGATGTATCCGGGCTAAAT-CGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
1 AGTGATATATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
* * *
27744435 AGAGCATTCATGCTAGTGATGTATCCAGGCTGAATTCCGAAGAGCATTCGTGCT
66 AGAGCATTCATGCTAGTGATGTATCCAGGCTAAATTCCAAAGAGCATTCATGCT
* * * *
27744489 AGTGATATATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAATTCCGA
1 AGTGATATATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
* * ** * *
27744554 AGAGCATTCGTGCTAGTGATATATCC-GTGCTAAACCCCGAAGAGCATTCGTGCT
66 AGAGCATTCATGCTAGTGATGTATCCAG-GCTAAATTCCAAAGAGCATTCATGCT
* * * *
27744608 GGTGTTATGTCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGT-CCGAAGAGCA
27744640 ATCATGCTGG
Statistics
Matches: 245, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
118 113 0.46
119 103 0.42
120 29 0.12
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (119 bp):
AGTGATATATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
AGAGCATTCATGCTAGTGATGTATCCAGGCTAAATTCCAAAGAGCATTCATGCT
Found at i:27746131 original size:43 final size:41
Alignment explanation
Indices: 27746068--27746150 Score: 123
Period size: 44 Copynumber: 2.0 Consensus size: 41
27746058 GTATGTAGTG
*
27746068 AAATCCTCATGTTTACGTGATTGG-TTAATGAAGTCTTTGA
1 AAATCCTCATGTTTACGTGATTGGTTTAATGAAATCTTTGA
27746108 AAATCCCTCATGGTTTAACGTGATTGGTTTAATGAAATCTTTG
1 AAAT-CCTCAT-GTTT-ACGTGATTGGTTTAATGAAATCTTTG
27746151 TTACCTTGGC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
40 4 0.11
41 6 0.16
42 4 0.11
43 10 0.26
44 14 0.37
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (41 bp):
AAATCCTCATGTTTACGTGATTGGTTTAATGAAATCTTTGA
Found at i:27754685 original size:39 final size:39
Alignment explanation
Indices: 27754589--27754728 Score: 142
Period size: 40 Copynumber: 3.5 Consensus size: 39
27754579 ATGATGTCTG
* * * *
27754589 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCC
27754628 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GG-CTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCC
* * *
27754668 GGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTTTAA-CC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC-TAAATCC
*
27754707 GGGCTATGTCCCGAAGGCATTT
1 -GGCTAAGTCCCGAAGGCATTT
27754729 TGAACGAGTA
Statistics
Matches: 86, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
38 1 0.01
39 30 0.35
40 47 0.55
41 8 0.09
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
Found at i:27755045 original size:46 final size:47
Alignment explanation
Indices: 27754955--27755066 Score: 192
Period size: 46 Copynumber: 2.4 Consensus size: 47
27754945 AGGGTGTGGT
*
27754955 AATGTGAAAGTGTATATATGTTGATAGGTCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTTGATAGGCCTAATGGCCGATGTGATG
27755002 AATGTGAAAGTGTATATATG-TGATAAGGCCTAATGG-CGATGTGATG
1 AATGTGAAAGTGTATATATGTTGAT-AGGCCTAATGGCCGATGTGATG
27755048 AATGTGAAAGTGTATATAT
1 AATGTGAAAGTGTATATAT
27755067 TGTATGTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
46 33 0.52
47 30 0.48
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTTGATAGGCCTAATGGCCGATGTGATG
Found at i:27761541 original size:40 final size:40
Alignment explanation
Indices: 27761458--27761720 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
27761448 TTGAATGCTG
* * * * * *
27761458 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
27761498 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
27761538 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
27761578 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
27761618 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
27761658 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
27761697 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
27761721 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:27761740 original size:79 final size:80
Alignment explanation
Indices: 27761497--27761755 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
27761487 AAGTGAATAT
* * * * * * *
27761497 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
27761561 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
27761577 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
27761642 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
27761657 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
27761721 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
27761736 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
27761756 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Found at i:27764343 original size:28 final size:27
Alignment explanation
Indices: 27764311--27764392 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 27
27764301 CCATTTACGT
27764311 ACCAAAACCTATACCATTTCGTACATAC
1 ACCAAAACCTATACCATTTCGTAC-TAC
*
27764339 ACC--AA---ATCCCATTTCG---TAC
1 ACCAAAACCTATACCATTTCGTACTAC
27764358 -C-AAAACCTATACCATTTCGTACCTAC
1 ACCAAAACCTATACCATTTCGTA-CTAC
27764384 ACCAAAACC
1 ACCAAAACC
27764393 CATTTCGTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 22
0.63 0.03 0.34
Matches are distributed among these distances:
18 1 0.02
19 5 0.12
22 10 0.24
23 10 0.24
26 5 0.12
27 1 0.02
28 9 0.22
ACGTcount: A:0.38, C:0.35, G:0.04, T:0.23
Consensus pattern (27 bp):
ACCAAAACCTATACCATTTCGTACTAC
Found at i:27764365 original size:45 final size:45
Alignment explanation
Indices: 27764299--27764418 Score: 195
Period size: 45 Copynumber: 2.6 Consensus size: 45
27764289 TGACCTTTTG
27764299 ACCCATTTACGTACCAAAACCTATACCATTTCGTACATACACCAAA
1 ACCCATTT-CGTACCAAAACCTATACCATTTCGTACATACACCAAA
* *
27764345 TCCCATTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
1 ACCCATTTCGTACCAAAACCTATACCATTTCGTACATACACCAAA
* *
27764390 ACCCATTTCGTACCTAAACTTATACCATT
1 ACCCATTTCGTACCAAAACCTATACCATT
27764419 CCATAACTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
45 62 0.90
46 7 0.10
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.28
Consensus pattern (45 bp):
ACCCATTTCGTACCAAAACCTATACCATTTCGTACATACACCAAA
Found at i:27764375 original size:22 final size:22
Alignment explanation
Indices: 27764301--27764418 Score: 112
Period size: 23 Copynumber: 5.2 Consensus size: 22
27764291 ACCTTTTGAC
27764301 CCATTTACGTACCAAAACCTATA
1 CCATTT-CGTACCAAAACCTATA
* * *
27764324 CCATTTCGTA-CATACACCAAATC
1 CCATTTCGTACCA-AAACC-TATA
27764347 CCATTTCGTACCAAAACCTATA
1 CCATTTCGTACCAAAACCTATA
* * * *
27764369 CCATTTCGTACCTACACCAAAA
1 CCATTTCGTACCAAAACCTATA
* *
27764391 CCCATTTCGTACCTAAACTTATA
1 -CCATTTCGTACCAAAACCTATA
27764414 CCATT
1 CCATT
27764419 CCATAACTAA
Statistics
Matches: 77, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
21 2 0.03
22 33 0.43
23 40 0.52
24 2 0.03
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.28
Consensus pattern (22 bp):
CCATTTCGTACCAAAACCTATA
Found at i:27764437 original size:45 final size:44
Alignment explanation
Indices: 27764299--27764437 Score: 172
Period size: 45 Copynumber: 3.1 Consensus size: 44
27764289 TGACCTTTTG
27764299 ACCCATTTACGTACCAAAACCTATACCATTTCGT-ACATACACCAA
1 ACCCATTT-CGTACCAAAACCTATACCATTTCGTAAC-TACACCAA
*
27764344 ATCCCATTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
1 A-CCCATTTCGTACCAAAACCTATACCATTTCGTAACTACACC-AA
* * * * *
27764390 ACCCATTTCGTACCTAAACTTATACCATTCCATAACTAAACCTAA
1 ACCCATTTCGTACCAAAACCTATACCATTTCGTAACTACACC-AA
27764435 ACC
1 ACC
27764438 ATATTTGACC
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
45 72 0.87
46 11 0.13
ACGTcount: A:0.37, C:0.34, G:0.04, T:0.26
Consensus pattern (44 bp):
ACCCATTTCGTACCAAAACCTATACCATTTCGTAACTACACCAA
Found at i:27779249 original size:21 final size:23
Alignment explanation
Indices: 27779205--27779251 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
27779195 TCACCTGCAA
* *
27779205 TAAACACATTAAAATGAGTTTAT
1 TAAACACATGAAAATCAGTTTAT
27779228 TAAACACATGAAAA-CA-TTTAT
1 TAAACACATGAAAATCAGTTTAT
27779249 TAA
1 TAA
27779252 TCATACCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 1 0.05
23 13 0.59
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (23 bp):
TAAACACATGAAAATCAGTTTAT
Found at i:27781298 original size:19 final size:17
Alignment explanation
Indices: 27781248--27781289 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
27781238 GACTTTCATC
27781248 TTTTCCACTCT-TTTCT
1 TTTTCCACTCTCTTTCT
*
27781264 TTTTCAACTTCTCTTTCT
1 TTTTCCAC-TCTCTTTCT
27781282 TTTTCCAC
1 TTTTCCAC
27781290 AATCTCTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 7 0.32
17 3 0.14
18 12 0.55
ACGTcount: A:0.10, C:0.31, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTCCACTCTCTTTCT
Found at i:27784376 original size:15 final size:14
Alignment explanation
Indices: 27784356--27784403 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
27784346 ACTCTCATTT
27784356 TCTTTTTCTTTTATC
1 TCTTTTTCTTTT-TC
27784371 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTC
* *
27784385 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTC
27784400 TCTT
1 TCTT
27784404 CTCAGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (14 bp):
TCTTTTTCTTTTTC
Found at i:27784395 original size:21 final size:21
Alignment explanation
Indices: 27784341--27784406 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
27784331 CTCACTCTCA
*
27784341 CTCTCACTCTCATTTTCTTTTT
1 CTCTCA-TCTCTTTTTCTTTTT
* *
27784363 CTTTTATCTCTTTTTCTTTTT
1 CTCTCATCTCTTTTTCTTTTT
* *
27784384 CTCTCATTTCTTTTT-TTCTT
1 CTCTCATCTCTTTTTCTTTTT
27784404 CTC
1 CTC
27784407 AGAATTTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
20 7 0.19
21 26 0.70
22 4 0.11
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (21 bp):
CTCTCATCTCTTTTTCTTTTT
Found at i:27785543 original size:31 final size:32
Alignment explanation
Indices: 27785485--27785551 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
27785475 TTTTTTTCAA
27785485 TTACAATATCGTAATGCCGAAAATGTCGATTC
1 TTACAATATCGTAATGCCGAAAATGTCGATTC
27785517 TTACAATATCGTAATGCCG-AAATGTCGATTC
1 TTACAATATCGTAATGCCGAAAATGTCGATTC
27785548 TTAC
1 TTAC
27785552 TCCGATTCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 16 0.46
32 19 0.54
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (32 bp):
TTACAATATCGTAATGCCGAAAATGTCGATTC
Found at i:27791785 original size:5 final size:5
Alignment explanation
Indices: 27791775--27791799 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
27791765 GTCTGAAATT
27791775 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
27791800 CTCAATGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:27795630 original size:37 final size:37
Alignment explanation
Indices: 27795580--27795731 Score: 250
Period size: 37 Copynumber: 4.1 Consensus size: 37
27795570 ACCTTTAGCT
* * *
27795580 CGGACGTAATCTCCACACGAAGTTATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
*
27795617 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
*
27795654 CAGACATAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
*
27795691 CGGACATAATCTCCACACGTAGTCATCGGGTCTCACC
1 CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
27795728 CGGA
1 CGGA
27795732 ATATATTTCC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 107 1.00
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (37 bp):
CGGACATAATCTCCACACGTAGTCATCGGGTCTTACC
Found at i:27795946 original size:47 final size:47
Alignment explanation
Indices: 27795894--27796010 Score: 162
Period size: 47 Copynumber: 2.5 Consensus size: 47
27795884 TTTCACACTA
* ** *
27795894 GCCATTCGGCTTTACCGCATATATGCATTTTCATATTCACCACATTG
1 GCCATTCGGCTTTACCACATATATGCATGCTCACATTCACCACATTG
* * * *
27795941 GCCATTCGGCCTTATCACATATATGCATGCTCACATTTATCACATTG
1 GCCATTCGGCTTTACCACATATATGCATGCTCACATTCACCACATTG
27795988 GCCATTCGGCTTTACCACATATA
1 GCCATTCGGCTTTACCACATATA
27796011 CATATCACAC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (47 bp):
GCCATTCGGCTTTACCACATATATGCATGCTCACATTCACCACATTG
Found at i:27796049 original size:48 final size:48
Alignment explanation
Indices: 27795980--27796254 Score: 388
Period size: 48 Copynumber: 5.6 Consensus size: 48
27795970 CTCACATTTA
*
27795980 TCACATTGGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
* * * * *
27796028 TCACATTAGCCATTCGACTTTACCACCTATACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
*
27796076 TCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
* * * * *
27796124 TCACATTAGCCATTCGGCCTTATCACACATATATATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTA-C-CACATATACATATCACACATATATT
*
27796174 TCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
*
27796222 TCACATTAGCCATTCGGCCTTATCACACATATA
1 TCACATTAGCCATTCGGCTTTA-C-CACATATA
27796255 TATACGGGTT
Statistics
Matches: 197, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
48 145 0.74
49 3 0.02
50 49 0.25
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (48 bp):
TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
Found at i:27796213 original size:98 final size:97
Alignment explanation
Indices: 27795934--27796258 Score: 507
Period size: 98 Copynumber: 3.4 Consensus size: 97
27795924 TCATATTCAC
* ** *
27795934 CACATTGGCCATTCGGCCTTAT-CACATATATGCATGCTC--ACAT-TTATCACATTGGCCATTC
1 CACATTAGCCATTCGGCCTTATCCACATATATATAT-CTCATACATATT-TCACATTCGCCATTC
27795995 GGCTTTACCACATATACATATCACACATATATTT
64 GGCTTTACCACATATACATATCACACATATATTT
* * * *
27796029 CACATTAGCCATTCGACTTTA-CCACCTATACATATCTCATACATATTTCACATTCGCCATTCGG
1 CACATTAGCCATTCGGCCTTATCCACATATATATATCTCATACATATTTCACATTCGCCATTCGG
27796093 CTTTACCACATATACATATCACACATATATTT
66 CTTTACCACATATACATATCACACATATATTT
27796125 CACATTAGCCATTCGGCCTTATCACACATATATATATCTCATACATATTTCACATTCGCCATTCG
1 CACATTAGCCATTCGGCCTTATC-CACATATATATATCTCATACATATTTCACATTCGCCATTCG
27796190 GCTTTACCACATATACATATCACACATATATTT
65 GCTTTACCACATATACATATCACACATATATTT
27796223 CACATTAGCCATTCGGCCTTATCACACATATATATA
1 CACATTAGCCATTCGGCCTTATC-CACATATATATA
27796259 CGGGTTCACA
Statistics
Matches: 212, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
94 3 0.01
95 27 0.13
96 71 0.33
97 3 0.01
98 108 0.51
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (97 bp):
CACATTAGCCATTCGGCCTTATCCACATATATATATCTCATACATATTTCACATTCGCCATTCGG
CTTTACCACATATACATATCACACATATATTT
Found at i:27796325 original size:98 final size:97
Alignment explanation
Indices: 27795934--27796304 Score: 380
Period size: 98 Copynumber: 3.8 Consensus size: 97
27795924 TCATATTCAC
* ** *
27795934 CACATTGGCCATTCGGCCTTAT--CACATATATGCAT-GC-T-CACATTTATCACATTGGCCATT
1 CACATTAGCCATTCGGCCTTATCACACATATATATATCGCATACACA-TT-TCACATTCGCCATT
* * *
27795994 CGGCTTTACCACATATACATATCACACATATATTT
64 CGGCCTTACCACATACACATATCACACATACA-TT
* * * * * *
27796029 CACATTAGCCATTCGACTTTA-C-CACCTATACATATCTCATACATATTTCACATTCGCCATTCG
1 CACATTAGCCATTCGGCCTTATCACACATATATATATCGCATACACATTTCACATTCGCCATTCG
* * *
27796092 GCTTTACCACATATACATATCACACATATATTT
66 GCCTTACCACATACACATATCACACATACA-TT
* *
27796125 CACATTAGCCATTCGGCCTTATCACACATATATATATCTCATACATATTTCACATTCGCCATTCG
1 CACATTAGCCATTCGGCCTTATCACACATATATATATCGCATACACATTTCACATTCGCCATTCG
* * *
27796190 GCTTTACCACATATACATATCACACATATATTT
66 GCCTTACCACATACACATATCACACATACA-TT
** * *
27796223 CACATTAGCCATTCGGCCTTATCACACATATATATA-CGGGTTCACATTCATCACATTGGCCATT
1 CACATTAGCCATTCGGCCTTATCACACATATATATATCGCATACACATT--TCACATTCGCCATT
27796287 CGGCCTTATCACACATAC
64 CGGCCTTA-C-CACATAC
27796305 GCATGTTCAC
Statistics
Matches: 244, Mismatches: 22, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
95 27 0.11
96 68 0.28
97 11 0.05
98 111 0.45
99 20 0.08
100 1 0.00
101 6 0.02
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (97 bp):
CACATTAGCCATTCGGCCTTATCACACATATATATATCGCATACACATTTCACATTCGCCATTCG
GCCTTACCACATACACATATCACACATACATT
Done.