Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, whole genome shotgun sequence
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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 17 of 100
Found at i:3188260 original size:24 final size:24
Alignment explanation
Indices: 3188231--3188279 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3188221 AATTTTGCAG
*
3188231 TGTAATCTGTAAGGCAAATTTCAC
1 TGTAATCTCTAAGGCAAATTTCAC
*
3188255 TGTAATCTCTAAGGCAGATTTCAC
1 TGTAATCTCTAAGGCAAATTTCAC
3188279 T
1 T
3188280 ATCTCCAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (24 bp):
TGTAATCTCTAAGGCAAATTTCAC
Found at i:3193644 original size:197 final size:196
Alignment explanation
Indices: 3193297--3193690 Score: 510
Period size: 197 Copynumber: 2.0 Consensus size: 196
3193287 CACAAGTTTG
* * * *
3193297 AGATTAAATCTCAACTTATATATTATATCATATTTACACATCTTCTAATGTGGGATTGGTGGCGT
1 AGATTAAATATCAACTTATATATTATACCATATTCACACATCTTCTAATGTGAGATTGGTGGCGT
* * * * *
3193362 CACAATCTCCTTACCTTTAAAACTTGACATTCCTGTTAAGTCGAGTTCAACTATAGAATCAAGAT
66 CACAATCTCCTCACCTTTAAAACTTGACATTCCTGTCAAGTCGAGTCCAACCAAAGAATCAAGAT
* * *
3193427 CACATTAGATGTTGAGATTCTAGAGATAACTCCCAACCATGTAATACTTAATAACTCCCACAATG
131 AACATTAGACGTTAAGATTCTAGAGATAACTCCCAACCATGTAATACTTAATAACTCCCACAATG
3193492 T
196 T
* *
3193493 AGATTAAATATCAACTTATATATTATACCATATTCACATATTCTTCTAATGTGAGATT-GTGGGT
1 AGATTAAATATCAACTTATATATTATACCATATTCACACA-TCTTCTAATGTGAGATTGGT-GGC
* *
3193557 GTCACAATCT-CTCCACCTTTAAAACTTGACA-TCCTTGTCAAGTTGAGTCCAACCACAAGACT-
64 GTCACAATCTCCT-CACCTTTAAAACTTGACATTCC-TGTCAAGTCGAGTCCAACCA-AAGAATC
* ** * *
3193619 AAGATAACATTTA-ACGTTAAGATTCTAGAGGTGGCTCCCAACCATGTAATACTTAGTTACTCCC
126 AAGATAACA-TTAGACGTTAAGATTCTAGAGATAACTCCCAACCATGTAATACTTAATAACTCCC
3193683 ACAATGT
190 ACAATGT
3193690 A
1 A
3193691 ACACTTAGTT
Statistics
Matches: 171, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
196 43 0.25
197 121 0.71
198 7 0.04
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (196 bp):
AGATTAAATATCAACTTATATATTATACCATATTCACACATCTTCTAATGTGAGATTGGTGGCGT
CACAATCTCCTCACCTTTAAAACTTGACATTCCTGTCAAGTCGAGTCCAACCAAAGAATCAAGAT
AACATTAGACGTTAAGATTCTAGAGATAACTCCCAACCATGTAATACTTAATAACTCCCACAATG
T
Found at i:3193691 original size:24 final size:25
Alignment explanation
Indices: 3193653--3193700 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
3193643 CTAGAGGTGG
* *
3193653 CTCCCAACCATGTAATACTTAGTTA
1 CTCCCAACAATGTAACACTTAGTTA
3193678 CTCCC-ACAATGTAACACTTAGTT
1 CTCCCAACAATGTAACACTTAGTT
3193701 CCCGTCGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.31
Consensus pattern (25 bp):
CTCCCAACAATGTAACACTTAGTTA
Found at i:3195833 original size:59 final size:61
Alignment explanation
Indices: 3195757--3195873 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 61
3195747 TTTCTAATTA
* * * *
3195757 TGGTTAGATGGTATTATAGTGATTTTAGC-AATTATAATATGAGTGATATTTTCATAACCT
1 TGGTTAGATGGTATTATAGTAATTTTAGCAAATTATAATATGAGGGATACTTTAATAACCT
*
3195817 TGGTTAGA-GGTTTTATAGTAATTTTAGCAAATTATAATATGAGGGATACTTTAATAA
1 TGGTTAGATGGTATTATAGTAATTTTAGCAAATTATAATATGAGGGATACTTTAATAA
3195874 GTATGGTAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 18 0.35
60 33 0.65
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (61 bp):
TGGTTAGATGGTATTATAGTAATTTTAGCAAATTATAATATGAGGGATACTTTAATAACCT
Found at i:3196352 original size:26 final size:26
Alignment explanation
Indices: 3196322--3196383 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
3196312 AGGGTATGAC
* * * *
3196322 AATAATTTTAGTCAGAGAGGTATTTT
1 AATAATTTTAGTAAAAGAGATATTAT
* *
3196348 TATAATTATAGTAAAAGAGATATTAT
1 AATAATTTTAGTAAAAGAGATATTAT
3196374 AATAATTTTA
1 AATAATTTTA
3196384 AAAAATTATA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.42
Consensus pattern (26 bp):
AATAATTTTAGTAAAAGAGATATTAT
Found at i:3196885 original size:18 final size:18
Alignment explanation
Indices: 3196850--3196892 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
3196840 ATAATTTTTT
*
3196850 AAAAGAAAAAAAGTAAAA
1 AAAAGAAAAAAAGCAAAA
3196868 AAAAGAAACAAAA-CAAAA
1 AAAAGAAA-AAAAGCAAAA
3196886 AAGAAGA
1 AA-AAGA
3196893 GAAGGACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAAAGCAAAA
Found at i:3196886 original size:19 final size:18
Alignment explanation
Indices: 3196850--3196892 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3196840 ATAATTTTTT
**
3196850 AAAAGAAAAAAAGTAAAA
1 AAAAGAAAAAAACAAAAA
3196868 AAAAGAAACAAAACAAAAA
1 AAAAGAAA-AAAACAAAAA
*
3196887 AGAAGA
1 AAAAGA
3196893 GAAGGACCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAAACAAAAA
Found at i:3210000 original size:26 final size:27
Alignment explanation
Indices: 3209936--3210015 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
3209926 AATATAAGGA
* * * *
3209936 AATGATTCAATAAATTTTGGAGTAATT
1 AATGATTTAATGAATTTTGAAGTAATC
* *
3209963 AAAGTTTTAATGAATTTTGAAG-AATC
1 AATGATTTAATGAATTTTGAAGTAATC
*
3209989 AATGATTTAATGAATTCTTGATGTAAT
1 AATGATTTAATGAATT-TTGAAGTAAT
3210016 TATTTTGGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
26 17 0.40
27 22 0.52
28 3 0.07
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (27 bp):
AATGATTTAATGAATTTTGAAGTAATC
Found at i:3211078 original size:46 final size:46
Alignment explanation
Indices: 3211028--3211269 Score: 167
Period size: 46 Copynumber: 5.4 Consensus size: 46
3211018 GTTGATAATT
* ** ** *
3211028 TTTTGAAAATAAATTTAGAAGTTTTTTTAAGAAAAGGTTAAACAAC
1 TTTTGAAAATAAATTTAAAAACTCATTTAAGAAAAGGCTAAACAAC
* * **
3211074 TTTTGAAAATAAATTTAAAAACTCATTTAAGCAAAGGCTCAATGAC
1 TTTTGAAAATAAATTTAAAAACTCATTTAAGAAAAGGCTAAACAAC
* * * **
3211120 TTTTGAAAATAAATTTAAAAGCTTC-TTGAAGCAAAA-GCTCAATGAC
1 TTTTGAAAATAAATTTAAAAAC-TCATTTAAG-AAAAGGCTAAACAAC
* * *
3211166 TTTTGAAAACAAATTTAAAAGCTTC-TTTAAG---A--CTTAACAAC
1 TTTTGAAAATAAATTTAAAAAC-TCATTTAAGAAAAGGCTAAACAAC
* * * * * * * *
3211207 TTTTGAAAACAAATTTAAAAACTCCTTTAAGCAAGGGATCAATAAT
1 TTTTGAAAATAAATTTAAAAACTCATTTAAGAAAAGGCTAAACAAC
3211253 TTTTGAAAATAAATTTA
1 TTTTGAAAATAAATTTA
3211270 GAATCCTAGT
Statistics
Matches: 163, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
40 2 0.01
41 33 0.20
42 1 0.01
46 122 0.75
47 5 0.03
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (46 bp):
TTTTGAAAATAAATTTAAAAACTCATTTAAGAAAAGGCTAAACAAC
Found at i:3212697 original size:37 final size:37
Alignment explanation
Indices: 3212601--3212705 Score: 101
Period size: 36 Copynumber: 2.9 Consensus size: 37
3212591 CTCATTTTGT
* * *
3212601 GAGATTAGAAGTTGCTA-CTTTAGCCTAGAAATGTGA
1 GAGATGAGAGGTTGCTATCTTTAGCCTAGAAAAGTGA
* *
3212637 GAGATTAGAGTTTGCTATC-TTAGCCTA-AAAAGAT-A
1 GAGATGAGAGGTTGCTATCTTTAGCCTAGAAAAG-TGA
* *
3212672 GAGAGTGAGAGGTTGTTATCTTTAGCTTAGAAAA
1 GAGA-TGAGAGGTTGCTATCTTTAGCCTAGAAAA
3212706 CAAAGTGATT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
35 9 0.16
36 36 0.63
37 8 0.14
38 4 0.07
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (37 bp):
GAGATGAGAGGTTGCTATCTTTAGCCTAGAAAAGTGA
Found at i:3222627 original size:17 final size:17
Alignment explanation
Indices: 3222607--3222642 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3222597 ACAATGAGGC
3222607 AATCAATCCTATTTTGT
1 AATCAATCCTATTTTGT
* *
3222624 AATCAATCTTGTTTTGT
1 AATCAATCCTATTTTGT
3222641 AA
1 AA
3222643 ACTCTTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (17 bp):
AATCAATCCTATTTTGT
Found at i:3236981 original size:45 final size:46
Alignment explanation
Indices: 3236907--3237074 Score: 189
Period size: 46 Copynumber: 3.7 Consensus size: 46
3236897 GTTGTTAAGT
*
3236907 CTTAAAGAAGCTTTTAAATTTGTTTTCAAAAGTCATTGAGCTTTTG
1 CTTAAAGAAGCTTTTAAATTTGTTTTCAAAAGTCATTGAGCCTTTG
* * *
3236953 CTTCAAGAAGCTTTT-AATTTATTTTCAAAATTCATTGAGCCTTTG
1 CTTAAAGAAGCTTTTAAATTTGTTTTCAAAAGTCATTGAGCCTTTG
* ** * * *
3236998 CTTAAATG-AGTTTTTAAATTTGTTTTCAAAAGTTGTTTAACCTTTT
1 CTTAAA-GAAGCTTTTAAATTTGTTTTCAAAAGTCATTGAGCCTTTG
* *
3237044 CTTAAAAGAA-CTTCTAAATTTATTTTCAAAA
1 CTT-AAAGAAGCTTTTAAATTTGTTTTCAAAA
3237075 AATTATCAAC
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
45 38 0.37
46 60 0.59
47 4 0.04
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (46 bp):
CTTAAAGAAGCTTTTAAATTTGTTTTCAAAAGTCATTGAGCCTTTG
Found at i:3237042 original size:46 final size:45
Alignment explanation
Indices: 3236835--3237074 Score: 163
Period size: 46 Copynumber: 5.4 Consensus size: 45
3236825 ACTAGGATTC
* * * * * * *
3236835 TAAATTTATTTTAAAAAATTATTGATCCCTTGTTTAAAGGAGTTTT
1 TAAATTTGTTTTCAAAAGTTATTGAACCTTTGCTTAAA-GAGCTTT
* * *
3236881 TAAATTGGTTTT-AAAAGTTGTT-AA---GT-CTTAAAGAAGCTTT
1 TAAATTTGTTTTCAAAAGTTATTGAACCTTTGCTTAAAG-AGCTTT
* * * *
3236921 TAAATTTGTTTTCAAAAGTCATTGAGCTTTTGCTTCAAGAAGCTTT
1 TAAATTTGTTTTCAAAAGTTATTGAACCTTTGCTTAAAG-AGCTTT
* * *
3236967 T-AATTTATTTTCAAAA-TTCATTGAGCCTTTGCTTAAATGAGTTTT
1 TAAATTTGTTTTCAAAAGTT-ATTGAACCTTTGCTTAAA-GAGCTTT
* * * * *
3237012 TAAATTTGTTTTCAAAAGTTGTTTAACCTTTTCTTAAAAGAACTTC
1 TAAATTTGTTTTCAAAAGTTATTGAACCTTTGCTT-AAAGAGCTTT
*
3237058 TAAATTTATTTTCAAAA
1 TAAATTTGTTTTCAAAA
3237075 AATTATCAAC
Statistics
Matches: 154, Mismatches: 28, Indels: 24
0.75 0.14 0.12
Matches are distributed among these distances:
39 1 0.01
40 21 0.14
41 9 0.06
42 1 0.01
44 2 0.01
45 45 0.29
46 70 0.45
47 5 0.03
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.46
Consensus pattern (45 bp):
TAAATTTGTTTTCAAAAGTTATTGAACCTTTGCTTAAAGAGCTTT
Found at i:3239216 original size:17 final size:17
Alignment explanation
Indices: 3239190--3239222 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3239180 CATCATCATC
3239190 AATTATCATTA-TTATT
1 AATTATCATTAGTTATT
3239206 AATTCATCATTAGTTAT
1 AATT-ATCATTAGTTAT
3239223 AGTCACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTATCATTAGTTATT
Found at i:3240950 original size:313 final size:303
Alignment explanation
Indices: 3240305--3240950 Score: 771
Period size: 314 Copynumber: 2.1 Consensus size: 303
3240295 GAATGGATGC
* * * *
3240305 TTGAAGGCATTTTTGGCTCAAAATGCCTTTAATATTCCAGATGATAAATTTTAATGATCGGATTA
1 TTGAAGGCAATTTTGGTTAAAAATGCCTTTAATATTCCAGATAATAAATTTTAATGATCGGATTA
* * * **
3240370 TTGAAGACGGCTATATCTAAAAACTCTTTCAATAATATTTTATTAGAAATTATTCAAGGCATTAC
66 TTAAAGACGGCTATATCTAAAAACCCTTTCAATAACATTTTATTAGAAAGCATTCAAGGCATTAC
* * *
3240435 CTGTAGAAAAACGTCATTCATAATCCATTCGATTAATTTTTAATTGGTATTATTGAAGGTATTTT
131 CCGTAGAAAAACGTCATTCATAATCCATTCAATTAATTTTTAATTAGTATTATTGAAGGTATTTT
** * *
3240500 TTAAAATGCCTTCAATAATTTATACAAAAAAGATGAGATAGATTCTTAAAGGTATTTTTTGTCCA
196 TTAAAATGCCTTCAATAATCCACACAAAAAAGATGAGACAGATTCTTAAAGGTATTTTTTGTCCA
* *
3240565 AAATACCTTTAATATTCCACACAATAAATTGTTGGGGGGAGTA
261 AAATACCTTTAATATTCCACACAATAAATTGTTAGGAGGAGTA
* * * *
3240608 TTGAAGGCGATTTTGGTAAAAAGATGCCTTTAATATTCTAGATAATAAATTTTAATGGTCGGATT
1 TTGAAGGCAATTTTGGTTAAAA-ATGCCTTTAATATTCCAGATAATAAATTTTAATGATCGGATT
* * * *
3240673 ATTAAAGGCGGTTATATCTAGAAACGCCTTT-AATAACATTTTGTTAGGGTTATTCAAGGCATTT
65 ATTAAAGACGGCTATATCTAAAAAC-CCTTTCAATAACATTTTATTA--G--A---AA-GCA-TT
* * *
3240737 CAAGGCATTACCCGTAGGAAAATG-CATTTCATAATCTATTCAATTAATTTTTAATTAGTATTAT
120 CAAGGCATTACCCGTAGAAAAACGTCA-TTCATAATCCATTCAATTAATTTTTAATTAGTATTAT
* * *
3240801 TGAAGGTATTTTTTTAAAATGCCTTTAATAATCCACACAAAAAAGATGCA-ACGGATTCTTGAAG
184 TGAAGGTA-TTTTTTAAAATGCCTTCAATAATCCACACAAAAAAGATG-AGACAGATTCTTAAAG
* * * * *
3240865 GTATTTTTT-TACCTAAATCGCCTTTAATATTCCACACAATAAATTTTTAGGATGATTA
247 GTATTTTTTGT-CCAAAAT-ACCTTTAATATTCCACACAATAAATTGTTAGGAGGAGTA
*
3240923 TT-AAGGTAATTTTGGTTAAAAATGCCTT
1 TTGAAGGCAATTTTGGTTAAAAATGCCTT
3240951 AAAAATTTTC
Statistics
Matches: 287, Mismatches: 40, Indels: 22
0.82 0.11 0.06
Matches are distributed among these distances:
303 17 0.06
304 73 0.25
305 4 0.01
306 1 0.00
308 1 0.00
311 2 0.01
312 3 0.01
313 73 0.25
314 77 0.27
315 36 0.13
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (303 bp):
TTGAAGGCAATTTTGGTTAAAAATGCCTTTAATATTCCAGATAATAAATTTTAATGATCGGATTA
TTAAAGACGGCTATATCTAAAAACCCTTTCAATAACATTTTATTAGAAAGCATTCAAGGCATTAC
CCGTAGAAAAACGTCATTCATAATCCATTCAATTAATTTTTAATTAGTATTATTGAAGGTATTTT
TTAAAATGCCTTCAATAATCCACACAAAAAAGATGAGACAGATTCTTAAAGGTATTTTTTGTCCA
AAATACCTTTAATATTCCACACAATAAATTGTTAGGAGGAGTA
Found at i:3244438 original size:80 final size:80
Alignment explanation
Indices: 3244335--3244581 Score: 313
Period size: 80 Copynumber: 3.1 Consensus size: 80
3244325 AGAAATATCA
* * *
3244335 TTTAGCAAACCATTCAACATATGATTCAACCCCTCAATATCATACAATACCATTTAGCAAAACAA
1 TTTAACAAATCATTCAGCATATGATTCAACCCCTCAATATCATACAATACCATTTAGCAAAACAA
*
3244400 TATCAGACAACAAGG
66 TATTAGACAACAAGG
* *
3244415 TTTAACAAATCATTCAGCATATGATTCAATCCCC-CAATATCATACAATACCA-TTCGACAATAC
1 TTTAACAAATCATTCAGCATATGATTCAA-CCCCTCAATATCATACAATACCATTTAG-CAAAAC
3244478 AATATTAGACAACAA-G
64 AATATTAGACAACAAGG
* * ** * * *
3244494 TTCAACAAATGATTCAGCATACAATTCAGCCCCTTAATATCATACAATACCATTAAGCAAAA-AA
1 TTTAACAAATCATTCAGCATATGATTCAACCCCTCAATATCATACAATACCATTTAGCAAAACAA
* *
3244558 AATTAAACAACAAGG
66 TATTAGACAACAAGG
3244573 TTTAACAAA
1 TTTAACAAA
3244582 CCATAATATT
Statistics
Matches: 144, Mismatches: 18, Indels: 11
0.83 0.10 0.06
Matches are distributed among these distances:
78 17 0.12
79 58 0.40
80 65 0.45
81 4 0.03
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (80 bp):
TTTAACAAATCATTCAGCATATGATTCAACCCCTCAATATCATACAATACCATTTAGCAAAACAA
TATTAGACAACAAGG
Found at i:3246643 original size:32 final size:31
Alignment explanation
Indices: 3246607--3246666 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
3246597 TATTTTTGTT
* *
3246607 TTTTTTTTTTGTTAACTTTTTTATATTTTATA
1 TTTTTGTTTTATTAACTTTTTTA-ATTTTATA
*
3246639 TTTTTGTTTTATTAATTTTTTTAATTTT
1 TTTTTGTTTTATTAACTTTTTTAATTTT
3246667 TGGGCCCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 5 0.20
32 20 0.80
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (31 bp):
TTTTTGTTTTATTAACTTTTTTAATTTTATA
Found at i:3246945 original size:28 final size:28
Alignment explanation
Indices: 3246897--3246965 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
3246887 TTATAGATTT
* *
3246897 ATTTTTTTGTTTTGGATTCTTTTTGAATC
1 ATTTTTTTTTTTTGGAGTCTTTTT-AATC
* *
3246926 ATTTTTTTTTTTTGG-GTCTTTTTTATG
1 ATTTTTTTTTTTTGGAGTCTTTTTAATC
*
3246953 AGTTTTTTTTTTT
1 ATTTTTTTTTTTT
3246966 ACTATTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 14 0.40
28 7 0.20
29 14 0.40
ACGTcount: A:0.10, C:0.04, G:0.13, T:0.72
Consensus pattern (28 bp):
ATTTTTTTTTTTTGGAGTCTTTTTAATC
Found at i:3247998 original size:52 final size:52
Alignment explanation
Indices: 3247920--3248076 Score: 235
Period size: 52 Copynumber: 3.0 Consensus size: 52
3247910 TATAACCATA
* *
3247920 CAAACTTGCCCATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTATAAGT
* *
3247972 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTACAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTATAAGT
* * *
3248024 CAAACTTACCTATTAAGAATCCTCTTT-CTCTTGGAATTCTTCTTTTATAAGT
1 CAAACTTGCCTATTAAGAATCC-CTTTCCTCTTAGAATTCTTCTCTTATAAGT
3248076 C
1 C
3248077 TTCTTTCCAT
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
52 91 0.96
53 4 0.04
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.41
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTATAAGT
Found at i:3248328 original size:20 final size:20
Alignment explanation
Indices: 3248300--3248337 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3248290 TAACTGTGTA
3248300 TATTAAATTAT-ATTTTATAT
1 TATTAAATT-TCATTTTATAT
*
3248320 TATTTAATTTCATTTTAT
1 TATTAAATTTCATTTTAT
3248338 TTGTGTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTAAATTTCATTTTATAT
Found at i:3250607 original size:112 final size:112
Alignment explanation
Indices: 3250410--3250634 Score: 450
Period size: 112 Copynumber: 2.0 Consensus size: 112
3250400 AAATTAATCA
3250410 AATATTTAACTTTTAAAGAGGTGCTTCATAGTTTAGAAATTTTTTGCATTCAAAAGGGATTTTTG
1 AATATTTAACTTTTAAAGAGGTGCTTCATAGTTTAGAAATTTTTTGCATTCAAAAGGGATTTTTG
3250475 AGTCAAAAAGTGAGGTATCTTCTTGACTGAAATTAATAGGATTGGAT
66 AGTCAAAAAGTGAGGTATCTTCTTGACTGAAATTAATAGGATTGGAT
3250522 AATATTTAACTTTTAAAGAGGTGCTTCATAGTTTAGAAATTTTTTGCATTCAAAAGGGATTTTTG
1 AATATTTAACTTTTAAAGAGGTGCTTCATAGTTTAGAAATTTTTTGCATTCAAAAGGGATTTTTG
3250587 AGTCAAAAAGTGAGGTATCTTCTTGACTGAAATTAATAGGATTGGAT
66 AGTCAAAAAGTGAGGTATCTTCTTGACTGAAATTAATAGGATTGGAT
3250634 A
1 A
3250635 GAATGCTAGA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 113 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (112 bp):
AATATTTAACTTTTAAAGAGGTGCTTCATAGTTTAGAAATTTTTTGCATTCAAAAGGGATTTTTG
AGTCAAAAAGTGAGGTATCTTCTTGACTGAAATTAATAGGATTGGAT
Found at i:3252007 original size:2 final size:2
Alignment explanation
Indices: 3252000--3252024 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3251990 TTCTTTTCTT
3252000 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3252025 TAATCCGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3267016 original size:58 final size:57
Alignment explanation
Indices: 3266929--3267082 Score: 181
Period size: 57 Copynumber: 2.7 Consensus size: 57
3266919 TTGTGCAGAG
*
3266929 AAAATTGATACTTTCAACTTTTCCTCAAAAATCCA-TTTTT-GAAAACTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT--ATTTTTTGGAAAACTTA-TTTCAAGA
* * *
3266987 AAAATTGATACTTTCAACTTTT-TTCCAAAAATATTTTTTGGAAAGCTTATTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTGGAAAACTTATTTCAAGA
**
3267044 AAAATTGATACTTTCAACATTTT-CTTGAAAATATTTTTT
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTT
3267083 TCTTGAAATT
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
56 1 0.01
57 42 0.49
58 42 0.49
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAAACTTATTTCAAGA
Found at i:3267083 original size:58 final size:57
Alignment explanation
Indices: 3266928--3267083 Score: 183
Period size: 58 Copynumber: 2.7 Consensus size: 57
3266918 TTTGTGCAGA
* * *
3266928 GAAAATTGATACTTTCAACTTTTCCTCAAAAATCCATTTTTGAAAACTTATTTTTAAG
1 GAAAATTGATACTTTCAACTTTTCTTCAAAAAT-CTTTTTTGAAAACTTATTTTCAAG
* * *
3266986 AAAAATTGATACTTTCAACTTTT-TTCCAAAAATATTTTTTGGAAAGCTTA-TTTCAAG
1 GAAAATTGATACTTTCAACTTTTCTT-CAAAAATCTTTTTT-GAAAACTTATTTTCAAG
*
3267043 GAAAATTGATACTTTCAACATTTTCTTGAAAATAT-TTTTTT
1 GAAAATTGATACTTTCAAC-TTTTCTTCAAAA-ATCTTTTTT
3267084 CTTGAAATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
57 30 0.35
58 51 0.60
59 4 0.05
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (57 bp):
GAAAATTGATACTTTCAACTTTTCTTCAAAAATCTTTTTTGAAAACTTATTTTCAAG
Found at i:3267085 original size:17 final size:18
Alignment explanation
Indices: 3267063--3267101 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
3267053 ACTTTCAACA
3267063 TTTTCTTGAAAATATT-T
1 TTTTCTTGAAAATATTAT
*
3267080 TTTTCTTGAAATTATTAT
1 TTTTCTTGAAAATATTAT
3267098 TTTT
1 TTTT
3267102 ATTATTAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (18 bp):
TTTTCTTGAAAATATTAT
Found at i:3269974 original size:42 final size:41
Alignment explanation
Indices: 3269866--3270285 Score: 364
Period size: 41 Copynumber: 10.1 Consensus size: 41
3269856 ATAAACAAAG
* *
3269866 GCTCCTCTAAGCAGAGGCTCAACAACTTTGGAAAAATAAATAAA
1 GCTCCTCTAAGCAGAGGCTCAACGACTTT-GAAAAATAAAT--T
* * *
3269910 GGTCCTCTAAGCAGAGGTTCAACAACTTTGAAAAAATAAATT
1 GCTCCTCTAAGCAGAGGCTCAACGACTTTG-AAAAATAAATT
*
3269952 GCTTCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAGCAGAGGCTCAACGACTTT-GAAAAATAAATT
* * *
3269994 ACTCCTCTAAACAGAGGCTCAACGACTTTTGGAAGAATAAATT
1 GCTCCTCTAAGCAGAGGCTCAACGAC-TTT-GAAAAATAAATT
* * * * *
3270037 ACTCCTCTAATCAGAGGCTCAATGACTTTGGAAAATAAATG
1 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAATAAATT
* * *
3270078 GCTCCTCTAATCAGAGGCTCAACAACTTTG-AAAATAAATG
1 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAATAAATT
* * * *
3270118 GTTCCTCTAATCAGAGGCTCAACGACTTTGGAAAATAAATA
1 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAATAAATT
** * * * * *
3270159 AATTCTCTAAGCAGAAGCACCATGACTTT-AAAAATAAA-T
1 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAATAAATT
* * * * * * *
3270198 GCTCTTCTAAACAGAGGCACCACAATTTTGAAAAGTAAATT
1 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAATAAATT
* **
3270239 TCTCCTCTAAATAGAGG-T-AACCTCGACTTTTGAAAAATAAATT
1 GCTCCTCTAAGCAGAGGCTCAA---CGAC-TTTGAAAAATAAATT
3270282 GCTC
1 GCTC
3270286 ATTAACAATC
Statistics
Matches: 315, Mismatches: 51, Indels: 21
0.81 0.13 0.05
Matches are distributed among these distances:
39 21 0.07
40 54 0.17
41 81 0.26
42 64 0.20
43 58 0.18
44 37 0.12
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (41 bp):
GCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAATAAATT
Found at i:3270074 original size:84 final size:83
Alignment explanation
Indices: 3269866--3270173 Score: 370
Period size: 81 Copynumber: 3.7 Consensus size: 83
3269856 ATAAACAAAG
* * * *
3269866 GCTCCTCTAAGCAGAGGCTCAACAACTTTGGAAAAATAAATAAAGGTCCTCTAAGCAGAGGTTCA
1 GCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAAT-AA-CTCCTCTAAACAGAGGCTCA
*
3269931 ACAACTTTGAAAAAATAAATT
64 ACAACTTTG-GAAAATAAATT
* *
3269952 GCTTCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAATTACTCCTCTAAACAGAGGCTCAAC
1 GCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAATAACTCCTCTAAACAGAGGCTCAAC
*
3270017 GACTTTTGGAAGAATAAATT
66 AAC-TTTGGAA-AATAAATT
* * * ** *
3270037 ACTCCTCTAATCAGAGGCTCAATGACTTTGG-AAAATAAATGGCTCCTCTAATCAGAGGCTCAAC
1 GCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAATAACTCCTCTAAACAGAGGCTCAAC
*
3270101 AACTTT-GAAAATAAATG
66 AACTTTGGAAAATAAATT
* * * * *
3270118 GTTCCTCTAATCAGAGGCTCAACGACTTTGG-AAAATAAATAAATTCTCTAAGCAGA
1 GCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAATAACTCCTCTAAACAGA
3270174 AGCACCATGA
Statistics
Matches: 195, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
81 55 0.28
82 3 0.02
83 3 0.02
84 55 0.28
85 40 0.21
86 39 0.20
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (83 bp):
GCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAATAACTCCTCTAAACAGAGGCTCAAC
AACTTTGGAAAATAAATT
Found at i:3270086 original size:41 final size:41
Alignment explanation
Indices: 3269865--3270215 Score: 350
Period size: 42 Copynumber: 8.5 Consensus size: 41
3269855 AATAAACAAA
*
3269865 GGCTCCTCTAAGCAGAGGCTCAACAACTTTGGAAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGG-AAAATAAAT
* * *
3269907 AAAGG-TCCTCTAAGCAGAGGTTCAACAACTTTGAAAAAATAAAT
1 ---GGCTCCTCTAAGCAGAGGCTCAACGACTTTG-GAAAATAAAT
* *
3269951 TGCTTCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGG-AAAATAAAT
** *
3269993 TACTCCTCTAAACAGAGGCTCAACGACTTTTGGAAGAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGAC-TTTGGAA-AATAAAT
** * *
3270036 TACTCCTCTAATCAGAGGCTCAATGACTTTGGAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAATAAAT
* *
3270077 GGCTCCTCTAATCAGAGGCTCAACAACTTT-GAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAATAAAT
* *
3270117 GGTTCCTCTAATCAGAGGCTCAACGACTTTGGAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAATAAAT
*** * * * * * *
3270158 AAATTCTCTAAGCAGAAGCACCATGACTTT-AAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAATAAAT
* *
3270198 -GCTCTTCTAAACAGAGGC
1 GGCTCCTCTAAGCAGAGGC
3270216 ACCACAATTT
Statistics
Matches: 266, Mismatches: 34, Indels: 18
0.84 0.11 0.06
Matches are distributed among these distances:
39 12 0.05
40 47 0.18
41 65 0.24
42 67 0.25
43 37 0.14
44 36 0.14
45 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (41 bp):
GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAATAAAT
Found at i:3270187 original size:81 final size:82
Alignment explanation
Indices: 3269865--3270215 Score: 357
Period size: 81 Copynumber: 4.2 Consensus size: 82
3269855 AATAAACAAA
* **
3269865 GGCTCCTCTAAGCAGAGGCTCAACAACTTTGGAAAAATAAATAAAGGTCCTCTAAGCAGAGGTTC
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAATAAA--TCCTCTAAGCAGAGGCAC
*
3269930 AACAACTTTGAAAAAATAAAT
64 AACGACTTTG--AAAATAAAT
* * * * * *
3269951 TGCTTCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAATTACTCCTCTAAACAGAGGCTCAA
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAATAAATCCTCTAAGCAGAGGCACAA
3270016 CGACTTTTGGAAGAATAAAT
66 CGAC-TTT-GAA-AATAAAT
** * * *** * *
3270036 TACTCCTCTAATCAGAGGCTCAATGACTTTGG-AAAATAAATGGCTCCTCTAATCAGAGGCTCAA
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAATAAATCCTCTAAGCAGAGGCACAA
*
3270100 CAACTTTGAAAATAAAT
66 CGACTTTGAAAATAAAT
* * * * *
3270117 GGTTCCTCTAATCAGAGGCTCAACGACTTTGG-AAAATAAATAAATTCTCTAAGCAGAAGCACCA
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAATAAATCCTCTAAGCAGAGGCACAA
* *
3270181 TGACTTTAAAAATAAAT
66 CGACTTTGAAAATAAAT
* *
3270198 -GCTCTTCTAAACAGAGGC
1 GGCTCCTCTAAGCAGAGGC
3270216 ACCACAATTT
Statistics
Matches: 228, Mismatches: 34, Indels: 12
0.83 0.12 0.04
Matches are distributed among these distances:
80 15 0.07
81 73 0.32
82 3 0.01
83 3 0.01
84 55 0.24
85 38 0.17
86 41 0.18
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (82 bp):
GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAATAAATCCTCTAAGCAGAGGCACAA
CGACTTTGAAAATAAAT
Found at i:3270621 original size:44 final size:43
Alignment explanation
Indices: 3270563--3270666 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
3270553 TCAAGGCTTT
* *
3270563 TTAAAGGTTCTCATTTGGCAAACTTGGA-ATTCATATCCAAAAA
1 TTAAAGCTTCTCATTTGG-AAACTTGGAGATTCACATCCAAAAA
* **
3270606 TCTAAAGCTTTTCATTT-GAATTTTGGAGATTCACATCCAAAAA
1 T-TAAAGCTTCTCATTTGGAAACTTGGAGATTCACATCCAAAAA
3270649 TTCAAAGCTTCTCATTTG
1 TT-AAAGCTTCTCATTTG
3270667 AGTTCAAAGG
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
42 8 0.16
43 30 0.59
44 13 0.25
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (43 bp):
TTAAAGCTTCTCATTTGGAAACTTGGAGATTCACATCCAAAAA
Found at i:3272175 original size:9 final size:9
Alignment explanation
Indices: 3272161--3272220 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
3272151 AATTTGAATC
3272161 TTTTTTCAT
1 TTTTTTCAT
3272170 TTTTTTCA-
1 TTTTTTCAT
3272178 TTTTTTC-T
1 TTTTTTCAT
*
3272186 TTTTCCATCAT
1 TTTT--TTCAT
*
3272197 CTTCTTTTCTT
1 -TT-TTTTCAT
3272208 TTTTTTCAT
1 TTTTTTCAT
3272217 TTTT
1 TTTT
3272221 CATCTATTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
8 11 0.27
9 18 0.44
10 4 0.10
11 4 0.10
12 2 0.05
13 2 0.05
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:3277044 original size:60 final size:58
Alignment explanation
Indices: 3276906--3277074 Score: 239
Period size: 60 Copynumber: 2.9 Consensus size: 58
3276896 TTCAAGAAAG
* * * * **
3276906 TATTTTTAAAGAAAATTGATACTTTCAACTTTTCTTCAAAAATAATTTTTGGGAAGCT
1 TATTTTCAAAGAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTTAGAAGCT
3276964 TATTTTCAAAGAAAATTGATACTTTCAACTTTTCCTAAAAAAATATTTTTTTAGAGAGCT
1 TATTTTCAAAGAAAATTGATACTTTCAACTTTTCCT-AAAAAATATTTTTTTAGA-AGCT
* **
3277024 TATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTGAAAATATTTTTTT
1 TATTTTCAAAGAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTT
3277075 TTCTGAAATT
Statistics
Matches: 100, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
58 34 0.34
59 27 0.27
60 39 0.39
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (58 bp):
TATTTTCAAAGAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTTAGAAGCT
Found at i:3285702 original size:16 final size:16
Alignment explanation
Indices: 3285671--3285704 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3285661 ACAAATGATA
*
3285671 ATGATGATTTATGATG
1 ATGATGATTTACGATG
*
3285687 ATGATGATTTGCGATG
1 ATGATGATTTACGATG
3285703 AT
1 AT
3285705 TTTTAATGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.41
Consensus pattern (16 bp):
ATGATGATTTACGATG
Found at i:3285704 original size:19 final size:16
Alignment explanation
Indices: 3285665--3285696 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3285655 TGATAAACAA
3285665 ATGATAATGATGATTT
1 ATGATAATGATGATTT
*
3285681 ATGATGATGATGATTT
1 ATGATAATGATGATTT
3285697 GCGATGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (16 bp):
ATGATAATGATGATTT
Found at i:3287612 original size:28 final size:28
Alignment explanation
Indices: 3287572--3287652 Score: 119
Period size: 27 Copynumber: 2.9 Consensus size: 28
3287562 TTTGGTTAAG
3287572 AATGATTGTTTGAAATCTTACAAGTGCA
1 AATGATTGTTTGAAATCTTACAAGTGCA
* *
3287600 AATGATTGTTTG-AATTTTACAAGGGCA
1 AATGATTGTTTGAAATCTTACAAGTGCA
* *
3287627 AAAGATTGGTTGAAATCTTACAAGTG
1 AATGATTGTTTGAAATCTTACAAGTG
3287653 ATGATTTTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 23 0.50
28 23 0.50
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.35
Consensus pattern (28 bp):
AATGATTGTTTGAAATCTTACAAGTGCA
Found at i:3300088 original size:58 final size:57
Alignment explanation
Indices: 3299970--3300183 Score: 290
Period size: 58 Copynumber: 3.7 Consensus size: 57
3299960 TTTTGTGCAG
* * * *
3299970 GAAAAATTCATACTTTCAACTTTTCCTCAAAAATATTTTTTG-AAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAAC-TTATTTTCAA
*
3300027 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATCCA-TTTTTGAAAACTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAAT--ATTTTTTGAAAACTTATTTTCAA
*
3300085 GAAAAATTGATACTTTCAACTTTTT-TCCAAAAATATTTTTTGGAAAGCTTATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTTCT-CAAAAATATTTTTT-GAAAACTTATTTTCAA
* *
3300143 GGAAAATTGATACTTTCAACTTTTTCTCGAAAATATTTTTT
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTT
3300184 TTTCTTGAAA
Statistics
Matches: 141, Mismatches: 9, Indels: 13
0.87 0.06 0.08
Matches are distributed among these distances:
56 1 0.01
57 38 0.27
58 96 0.68
59 6 0.04
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (57 bp):
GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAACTTATTTTCAA
Found at i:3300187 original size:19 final size:20
Alignment explanation
Indices: 3300163--3300204 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3300153 TACTTTCAAC
3300163 TTTTTCTCGAAAATATT-TT
1 TTTTTCTCGAAAATATTATT
* *
3300182 TTTTTCTTGAAATTATTATT
1 TTTTTCTCGAAAATATTATT
3300202 TTT
1 TTT
3300205 ATTATTAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTTCTCGAAAATATTATT
Found at i:3303134 original size:42 final size:42
Alignment explanation
Indices: 3302946--3303409 Score: 429
Period size: 45 Copynumber: 11.0 Consensus size: 42
3302936 GGCTCAATAA
* * * *
3302946 CAGAGACTCAACAATTTTTGAAAAATAAACAAAGGCTCCTCTAAG
1 CAGAGGCTCAACAACTTTGGAAAAAT--A-AATGGCTCCTCTAAG
* *
3302991 CAGAGGCTTAACAACTTTGGAAAAATAAATAAAAGCTCCTCTAAG
1 CAGAGGCTCAACAACTTTGGAAAAATAAAT---GGCTCCTCTAAG
3303036 CAGAGGCTCAACAACTTTGGAAAAATAAATAAAGGCTCCTCTAAG
1 CAGAGGCTCAACAACTTTGGAAAAATAAAT---GGCTCCTCTAAG
* * * *
3303081 CAGAGGTTCAACAACTTTGAAAAAATAAATTGCTTCTCTAAG
1 CAGAGGCTCAACAACTTTGGAAAAATAAATGGCTCCTCTAAG
* ** *
3303123 CAGAGGCTCAACGACTTTGGAAAAATAAATTACTCCTCTAAA
1 CAGAGGCTCAACAACTTTGGAAAAATAAATGGCTCCTCTAAG
** *
3303165 CAGAGGCTCAATGACTTTTGGAAAAATAAATGGCTCCTCTAAT
1 CAGAGGCTCAACAAC-TTTGGAAAAATAAATGGCTCCTCTAAG
** *
3303208 CAGAGGCTCAATGACTTTGG-AAAATAAATGGCTCCTCTAAT
1 CAGAGGCTCAACAACTTTGGAAAAATAAATGGCTCCTCTAAG
* *
3303249 CAGAGGCTCAACAA-TTTTGAAAAATAAATGGCTCCTCTAAT
1 CAGAGGCTCAACAACTTTGGAAAAATAAATGGCTCCTCTAAG
* *** *
3303290 CAGAGGCTCAACGACTTTGG-AAAATAAATAAATTCTCTAAG
1 CAGAGGCTCAACAACTTTGGAAAAATAAATGGCTCCTCTAAG
* * * ** * *
3303331 CAGAAGCACCATGAC-TT-CAAAAATAAAT-GCTCCTCTAAA
1 CAGAGGCTCAACAACTTTGGAAAAATAAATGGCTCCTCTAAG
* * * * **
3303370 CAGAGGCACCACAA-TTTTGAAAAGTAAATTTCTCCTCTAA
1 CAGAGGCTCAACAACTTTGGAAAAATAAATGGCTCCTCTAA
3303410 ATAGAGGTAA
Statistics
Matches: 362, Mismatches: 47, Indels: 24
0.84 0.11 0.06
Matches are distributed among these distances:
39 20 0.06
40 24 0.07
41 103 0.28
42 71 0.20
43 40 0.11
45 104 0.29
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (42 bp):
CAGAGGCTCAACAACTTTGGAAAAATAAATGGCTCCTCTAAG
Found at i:3303244 original size:41 final size:41
Alignment explanation
Indices: 3302979--3303376 Score: 395
Period size: 41 Copynumber: 9.5 Consensus size: 41
3302969 AATAAACAAA
* *
3302979 GGCTCCTCTAAGCAGAGGCTTAACAACTTTGGAAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGG-AAAATAAAT
* *
3303021 AAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTGGAAAAATAAAT
1 ---GGCTCCTCTAAGCAGAGGCTCAACGACTTTGG-AAAATAAAT
* * *
3303066 AAAGGCTCCTCTAAGCAGAGGTTCAACAACTTTGAAAAAATAAAT
1 ---GGCTCCTCTAAGCAGAGGCTCAACGACTTTG-GAAAATAAAT
* *
3303111 TGCTTCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGG-AAAATAAAT
** * *
3303153 TACTCCTCTAAACAGAGGCTCAATGACTTTTGGAAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGAC-TTTGG-AAAATAAAT
* *
3303196 GGCTCCTCTAATCAGAGGCTCAATGACTTTGGAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAATAAAT
* * * *
3303237 GGCTCCTCTAATCAGAGGCTCAACAATTTTGAAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAATAAAT
*
3303278 GGCTCCTCTAATCAGAGGCTCAACGACTTTGGAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAATAAAT
*** * * * * * **
3303319 AAATTCTCTAAGCAGAAGCACCATGAC-TTCAAAAATAAAT
1 GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAATAAAT
*
3303359 -GCTCCTCTAAACAGAGGC
1 GGCTCCTCTAAGCAGAGGC
3303377 ACCACAATTT
Statistics
Matches: 310, Mismatches: 40, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
39 13 0.04
40 11 0.04
41 102 0.33
42 64 0.21
43 39 0.13
45 81 0.26
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (41 bp):
GGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAATAAAT
Found at i:3303407 original size:41 final size:41
Alignment explanation
Indices: 3302944--3303416 Score: 338
Period size: 41 Copynumber: 11.2 Consensus size: 41
3302934 GAGGCTCAAT
* **
3302944 AACAGAGACTCAACAATTTTTGAAAAATAAACAAAGGCTCCTCTA
1 AACAGAGGCTCAACAA-TTTTGAAAAAT--A-AATTGCTCCTCTA
* * * *
3302989 AGCAGAGGCTTAACAACTTTGGAAAAATAAATAAAAGCTCCTCTA
1 AACAGAGGCTCAACAA-TTTTGAAAAATAAAT---TGCTCCTCTA
* * *
3303034 AGCAGAGGCTCAACAACTTTGGAAAAATAAATAAAGGCTCCTCTA
1 AACAGAGGCTCAACAA-TTTTGAAAAATAAAT---TGCTCCTCTA
* * * *
3303079 AGCAGAGGTTCAACAACTTTGAAAAAATAAATTGCTTCTCTA
1 AACAGAGGCTCAACAATTTTG-AAAAATAAATTGCTCCTCTA
* * * *
3303121 AGCAGAGGCTCAACGACTTTGGAAAAATAAATTACTCCTCTA
1 AACAGAGGCTCAAC-AATTTTGAAAAATAAATTGCTCCTCTA
* * *
3303163 AACAGAGGCTCAATGACTTTTGGAAAAATAAATGGCTCCTCTA
1 AACAGAGGCTCAA-CAATTTT-GAAAAATAAATTGCTCCTCTA
* ** * * *
3303206 ATCAGAGGCTCAATGACTTTGGAAAATAAATGGCTCCTCTA
1 AACAGAGGCTCAACAATTTTGAAAAATAAATTGCTCCTCTA
* *
3303247 ATCAGAGGCTCAACAATTTTGAAAAATAAATGGCTCCTCTA
1 AACAGAGGCTCAACAATTTTGAAAAATAAATTGCTCCTCTA
* * * * *** *
3303288 ATCAGAGGCTCAACGACTTTGGAAAATAAATAAATTCTCTA
1 AACAGAGGCTCAACAATTTTGAAAAATAAATTGCTCCTCTA
* * * * ** * *
3303329 AGCAGAAGCACCATGA-CTTCAAAAATAAA-TGCTCCTCTA
1 AACAGAGGCTCAACAATTTTGAAAAATAAATTGCTCCTCTA
* * * *
3303368 AACAGAGGCACCACAATTTTGAAAAGTAAATTTCTCCTCTA
1 AACAGAGGCTCAACAATTTTGAAAAATAAATTGCTCCTCTA
*
3303409 AATAGAGG
1 AACAGAGG
3303417 TAACCTCGAC
Statistics
Matches: 356, Mismatches: 63, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
39 18 0.05
40 20 0.06
41 118 0.33
42 61 0.17
43 36 0.10
44 3 0.01
45 100 0.28
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (41 bp):
AACAGAGGCTCAACAATTTTGAAAAATAAATTGCTCCTCTA
Found at i:3310121 original size:57 final size:57
Alignment explanation
Indices: 3310058--3310270 Score: 268
Period size: 58 Copynumber: 3.7 Consensus size: 57
3310048 TTTGTGCAGA
* * *
3310058 AAAAATTGATACTTTCAACTTTTTTCT-AAAAATATTTTTT-GAAACTTTAATTTCGAG
1 AAAAATTGATACTTTCAAC-TTTTCCTAAAAAATATTTTTTAGAAAC-TTATTTTCAAG
** * *
3310115 AAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAAGCTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTAGAAA-CTTATTTTCAAG
* *
3310173 GAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTAGAGAGCTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTAGA-AACTTATTTTCAAG
* **
3310231 AAAAATTGATACTTTCAACTTTTTCTCGAAAATATTTTTT
1 AAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTT
3310271 TCTTAAAATT
Statistics
Matches: 137, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
56 5 0.04
57 32 0.23
58 98 0.72
59 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (57 bp):
AAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTAGAAACTTATTTTCAAG
Found at i:3310263 original size:116 final size:115
Alignment explanation
Indices: 3310059--3310270 Score: 320
Period size: 116 Copynumber: 1.8 Consensus size: 115
3310049 TTGTGCAGAA
* *
3310059 AAAATTGATACTTTCAACTTTTTTCTAAAAATATTTTTTGAAACTTTAATTTCGAGAAAAATTGA
1 AAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTGAAACTTTAATTTCAAGAAAAATTGA
3310124 TACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAAGCTTATTTTTAAGG
66 TACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAAGCTTATTTTTAAGG
* *
3310174 AAAATTGATACTTTCAAC-TTTTCCTAAAAAATATTTTTTAGAGAGC-TTATTTTCAAGAAAAAT
1 AAAATTGATACTTTCAACTTTTTCCT-AAAAATATTTTTT-GA-AACTTTAATTTCAAGAAAAAT
* * *
3310237 TGATACTTTCAACTTTTTCTCGAAAATATTTTTT
63 TGATACTTTCAACTTTTCCCCAAAAATATTTTTT
3310271 TCTTAAAATT
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
114 6 0.07
115 31 0.36
116 48 0.55
117 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (115 bp):
AAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTGAAACTTTAATTTCAAGAAAAATTGA
TACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAAGCTTATTTTTAAGG
Found at i:3310472 original size:75 final size:75
Alignment explanation
Indices: 3310383--3310534 Score: 261
Period size: 75 Copynumber: 2.0 Consensus size: 75
3310373 TCAAATCGGG
* *
3310383 AAAGAAAACATCTTACAAAAATTTGGATCATTTCT-AGATTTGTGCATGTCATCCTTGCGCAGGG
1 AAAGAAAACATCTTACAAAAATTTAGACCATTTCTCA-ATTTGTGCATGTCATCCTTGCGCAGGG
3310447 GCCATGCCTAC
65 GCCATGCCTAC
*
3310458 AAAGAAAACATCTTACAAAAATTTAGACCATTTCTCAATTTGTGCGTGTCATCCTTGCGCAGGGG
1 AAAGAAAACATCTTACAAAAATTTAGACCATTTCTCAATTTGTGCATGTCATCCTTGCGCAGGGG
3310523 CCATGCCTAC
66 CCATGCCTAC
3310533 AA
1 AA
3310535 CCTTCTTCTA
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
75 72 0.99
76 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (75 bp):
AAAGAAAACATCTTACAAAAATTTAGACCATTTCTCAATTTGTGCATGTCATCCTTGCGCAGGGG
CCATGCCTAC
Found at i:3311458 original size:25 final size:25
Alignment explanation
Indices: 3311424--3311473 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3311414 AAGGAGACAT
3311424 TGTTAGTGTGTTAGTGGTTGAAGCA
1 TGTTAGTGTGTTAGTGGTTGAAGCA
3311449 TGTTAGTGTGTTAGTGGTTGAAGCA
1 TGTTAGTGTGTTAGTGGTTGAAGCA
3311474 ACTAAGTATG
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:0.20, C:0.04, G:0.36, T:0.40
Consensus pattern (25 bp):
TGTTAGTGTGTTAGTGGTTGAAGCA
Found at i:3315747 original size:25 final size:25
Alignment explanation
Indices: 3315718--3315767 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3315708 CAAGGAGGAG
3315718 TGTTAGTGTGTTAGTGGTTGAAGCA
1 TGTTAGTGTGTTAGTGGTTGAAGCA
3315743 TGTTAGTGTGTTAGTGGTTGAAGCA
1 TGTTAGTGTGTTAGTGGTTGAAGCA
3315768 ACTAAGTATG
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:0.20, C:0.04, G:0.36, T:0.40
Consensus pattern (25 bp):
TGTTAGTGTGTTAGTGGTTGAAGCA
Found at i:3323709 original size:16 final size:16
Alignment explanation
Indices: 3323678--3323711 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3323668 ACAAATGATA
*
3323678 ATGATGATTTATGATG
1 ATGATGATTTACGATG
*
3323694 ATGATGATTTGCGATG
1 ATGATGATTTACGATG
3323710 AT
1 AT
3323712 TTTTAATGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.41
Consensus pattern (16 bp):
ATGATGATTTACGATG
Found at i:3323711 original size:19 final size:16
Alignment explanation
Indices: 3323672--3323703 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3323662 TGATAAACAA
3323672 ATGATAATGATGATTT
1 ATGATAATGATGATTT
*
3323688 ATGATGATGATGATTT
1 ATGATAATGATGATTT
3323704 GCGATGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (16 bp):
ATGATAATGATGATTT
Found at i:3323864 original size:24 final size:23
Alignment explanation
Indices: 3323836--3323885 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
3323826 TGACAAAACG
3323836 ATGATCTTGA-AATGTTTTGATATT
1 ATGAT-TTGAGAATGTTTTGA-ATT
3323860 ATGATTTGATGAATGTTTTGAATT
1 ATGATTTGA-GAATGTTTTGAATT
3323884 AT
1 AT
3323886 CTATATAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 4 0.17
24 10 0.42
25 10 0.42
ACGTcount: A:0.30, C:0.02, G:0.18, T:0.50
Consensus pattern (23 bp):
ATGATTTGAGAATGTTTTGAATT
Found at i:3339584 original size:16 final size:16
Alignment explanation
Indices: 3339563--3339593 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3339553 ACGATTGTTA
*
3339563 ATGATGATTTATGATT
1 ATGATGACTTATGATT
3339579 ATGATGACTTATGAT
1 ATGATGACTTATGAT
3339594 GATTTTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (16 bp):
ATGATGACTTATGATT
Found at i:3347419 original size:3 final size:3
Alignment explanation
Indices: 3347411--3347436 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3347401 TATATAAAAC
3347411 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3347437 CAAGTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3351816 original size:3 final size:3
Alignment explanation
Indices: 3351808--3351858 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
3351798 TAAAGCCTTG
3351808 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3351855 TTA T
1 TTA T
3351859 ATATCTTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3353641 original size:144 final size:142
Alignment explanation
Indices: 3353245--3353642 Score: 413
Period size: 144 Copynumber: 2.8 Consensus size: 142
3353235 CCTCAAAATA
* * *
3353245 TGTAAAATTACTAAAATACCTTTT-AGAGACATTTTCGTAATTTAACATTTTCGAGGTCGAATTT
1 TGTAAAATTACTAAAATACCTTTTAAG-GATATTTTCATAATTTAACATTTT-GAGGTTGAA-TT
* * * * * * *
3353309 TCAGGAAAAAC-TCCATACCATATTTTTATATTATTTCATGATTTATGGTACATTAAAAACCCTG
63 TCACG-AAAACTTTCAGATCATATTTTTATATTATTTCATAATTTTTGGCACATTAAAAACCCTG
*
3353373 ATCATACATTGAAAGG
127 ATCACACATTGAAAGG
* * * * ***
3353389 TGTTAAATTACCAAAATACCTTTTAAGGATATTTTCATAATTTGACTTTTTTGAGGTCTTTTTTT
1 TGTAAAATTACTAAAATACCTTTTAAGGATATTTTCATAATTTAAC-ATTTTGAGGT-TGAATTT
* * * * * *
3353454 TACAAAAACTTTCAGATTATATTTTTATGTTATTTCATAATTTTTGGCACATTGAAAACCTTGAT
64 CACGAAAACTTTCAGATCATATTTTTATATTATTTCATAATTTTTGGCACATTAAAAACCCTGAT
* *
3353519 TACACCTTGAAAGG
129 CACACATTGAAAGG
* * *
3353533 TGTAAAATTACTAAAATACCTTTTTAAGGGTATTTTCATAATTTAACCTTGTTGAGGTTGGATTT
1 TGTAAAATTACTAAAATACC-TTTTAAGGATATTTTCATAATTTAACATT-TTGAGGTTGAATTT
* * * *
3353598 CACGAAAACTTTAAGATCATGTTTTCATATTATTTTATAATTTTT
64 CACGAAAACTTTCAGATCATATTTTTATATTATTTCATAATTTTT
3353643 TATTCATTAA
Statistics
Matches: 206, Mismatches: 42, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
143 5 0.02
144 164 0.80
145 37 0.18
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (142 bp):
TGTAAAATTACTAAAATACCTTTTAAGGATATTTTCATAATTTAACATTTTGAGGTTGAATTTCA
CGAAAACTTTCAGATCATATTTTTATATTATTTCATAATTTTTGGCACATTAAAAACCCTGATCA
CACATTGAAAGG
Found at i:3358826 original size:20 final size:20
Alignment explanation
Indices: 3358773--3358826 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
3358763 TTTTATGGGT
* *
3358773 AAATCAATTGGTAATAATAA
1 AAATCTATTAGTAATAATAA
* *
3358793 AATTCT-GTAGGTAATAATAA
1 AAATCTATTA-GTAATAATAA
3358813 AAATCTATTAGTAA
1 AAATCTATTAGTAA
3358827 ATCTGTCGGT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.04
20 23 0.88
21 2 0.08
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (20 bp):
AAATCTATTAGTAATAATAA
Found at i:3359033 original size:6 final size:5
Alignment explanation
Indices: 3359013--3359116 Score: 52
Period size: 5 Copynumber: 19.8 Consensus size: 5
3359003 GTAATCAAAC
* * ***
3359013 TTTTA TTTTA TTTTTA CTTTTA TTTTA TTTT- TGTAA TCAAA TTTTTA
1 TTTTA TTTTA -TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA
**
3359060 TTTTA TTTTA -TTTA TCATTT- TTTTA TTATTA TCCTA TTATTA TTTTA
1 TTTTA TTTTA TTTTA T--TTTA TTTTA TT-TTA TTTTA TT-TTA TTTTA
3359107 TTTTTA TTTT
1 -TTTTA TTTT
3359117 TTCCTTTTCT
Statistics
Matches: 77, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
4 9 0.12
5 39 0.51
6 26 0.34
7 3 0.04
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:3359033 original size:17 final size:17
Alignment explanation
Indices: 3359011--3359044 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3359001 GTGTAATCAA
3359011 ACTTTTATTTTATTTTT
1 ACTTTTATTTTATTTTT
3359028 ACTTTTATTTTATTTTT
1 ACTTTTATTTTATTTTT
3359045 GTAATCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
ACTTTTATTTTATTTTT
Found at i:3359035 original size:12 final size:11
Alignment explanation
Indices: 3359013--3359116 Score: 58
Period size: 11 Copynumber: 9.8 Consensus size: 11
3359003 GTAATCAAAC
3359013 TTTTATTTTAT
1 TTTTATTTTAT
3359024 TTTTACTTTTA-
1 TTTTA-TTTTAT
3359035 TTTTA-TTT-T
1 TTTTATTTTAT
* * ***
3359044 TGTAATCAAAT
1 TTTTATTTTAT
3359055 TTTTATTTTA-
1 TTTTATTTTAT
3359065 TTTTA-TTTAT
1 TTTTATTTTAT
*
3359075 CATTT-TTTTAT
1 -TTTTATTTTAT
* **
3359086 TATTATCCTAT
1 TTTTATTTTAT
*
3359097 TATTATTTTAT
1 TTTTATTTTAT
3359108 TTTTATTTT
1 TTTTATTTT
3359117 TTCCTTTTCT
Statistics
Matches: 67, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
9 10 0.15
10 7 0.10
11 45 0.67
12 5 0.07
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:3359080 original size:42 final size:41
Alignment explanation
Indices: 3359002--3359116 Score: 126
Period size: 42 Copynumber: 2.8 Consensus size: 41
3358992 GTGTTCAAGG
*
3359002 TGTAATCAAACTTTTATTTTATTTTTACTTTTATTTTATTT-T
1 TGTAATCAAATTTTTATTTTATTTTTA-TTTTATTTT-TTTAT
3359044 TGTAATCAAATTTTTATTTTA-TTTTATTTATCATTTTTTTAT
1 TGTAATCAAATTTTTATTTTATTTTTATTT-T-ATTTTTTTAT
* * ** *
3359086 TATTATCCTATTATTATTTTATTTTTATTTT
1 TGTAATCAAATTTTTATTTTATTTTTATTTT
3359117 TTCCTTTTCT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
40 3 0.05
41 9 0.14
42 43 0.68
43 8 0.13
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (41 bp):
TGTAATCAAATTTTTATTTTATTTTTATTTTATTTTTTTAT
Found at i:3359099 original size:25 final size:26
Alignment explanation
Indices: 3359054--3359114 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
3359044 TGTAATCAAA
**
3359054 TTTTTATT-TTATTTTATTTATCATT
1 TTTTTATTATTATCCTATTTATCATT
*
3359079 TTTTTATTATTATCCTA-TTATTATT
1 TTTTTATTATTATCCTATTTATCATT
3359104 TTATTT-TTATT
1 TT-TTTATTATT
3359115 TTTTCCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 22 0.71
26 9 0.29
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (26 bp):
TTTTTATTATTATCCTATTTATCATT
Found at i:3361958 original size:31 final size:31
Alignment explanation
Indices: 3361922--3361984 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
3361912 TAGCACTTAG
3361922 TTTTCATTTTACTAATGATCGCTCTAATATT
1 TTTTCATTTTACTAATGATCGCTCTAATATT
*
3361953 TTTTCATTTTACTAATGATTGCTCTAATATT
1 TTTTCATTTTACTAATGATCGCTCTAATATT
3361984 T
1 T
3361985 ATGGATACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.54
Consensus pattern (31 bp):
TTTTCATTTTACTAATGATCGCTCTAATATT
Found at i:3365371 original size:18 final size:19
Alignment explanation
Indices: 3365348--3365387 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3365338 TTATATTTTT
3365348 ATTAATCAAATTGAATT-A
1 ATTAATCAAATTGAATTCA
* *
3365366 ATTAATCGAATTTAATTCA
1 ATTAATCAAATTGAATTCA
3365385 ATT
1 ATT
3365388 GATTAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTAATCAAATTGAATTCA
Found at i:3365584 original size:16 final size:16
Alignment explanation
Indices: 3365560--3365594 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3365550 AAATAATTTT
* *
3365560 TTATTTTATATTTTAA
1 TTATATTATATTTCAA
3365576 TTATATTATATTTCAA
1 TTATATTATATTTCAA
3365592 TTA
1 TTA
3365595 AAATTTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATTATATTTCAA
Found at i:3379422 original size:31 final size:31
Alignment explanation
Indices: 3379386--3379448 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
3379376 TAGCACTTAG
3379386 TTTTCATTTTACTAATGATCGCTCTAATATT
1 TTTTCATTTTACTAATGATCGCTCTAATATT
*
3379417 TTTTCATTTTACTAATGATTGCTCTAATATT
1 TTTTCATTTTACTAATGATCGCTCTAATATT
3379448 T
1 T
3379449 ATGGATACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.54
Consensus pattern (31 bp):
TTTTCATTTTACTAATGATCGCTCTAATATT
Found at i:3381545 original size:1 final size:1
Alignment explanation
Indices: 3381539--3381576 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
3381529 ATTAGAACAG
* *
3381539 AAAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3381577 CCGGGTCCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:3381959 original size:12 final size:12
Alignment explanation
Indices: 3381942--3381966 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3381932 TTATAAATCA
3381942 ATAAAAATTAAT
1 ATAAAAATTAAT
3381954 ATAAAAATTAAT
1 ATAAAAATTAAT
3381966 A
1 A
3381967 ATATGTAAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAAAATTAAT
Found at i:3383009 original size:16 final size:16
Alignment explanation
Indices: 3382990--3383024 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3382980 TATATATCTT
*
3382990 TTATTTTATATTTGAA
1 TTATATTATATTTGAA
*
3383006 TTATATTATATTTTAA
1 TTATATTATATTTGAA
3383022 TTA
1 TTA
3383025 AAATTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TTATATTATATTTGAA
Found at i:3383090 original size:15 final size:16
Alignment explanation
Indices: 3383068--3383104 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
3383058 AATCGAATTA
3383068 ATTAAAAATTAATTTTT
1 ATTAAAAATT-ATTTTT
3383085 -TTAAAAATTATTTTT
1 ATTAAAAATTATTTTT
3383100 ATTAA
1 ATTAA
3383105 TAGACCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTAAAAATTATTTTT
Found at i:3386252 original size:22 final size:22
Alignment explanation
Indices: 3386227--3386270 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3386217 TTATATATTT
*
3386227 ATATTTGCATTTTTAGAATTAA
1 ATATTTGCATTCTTAGAATTAA
*
3386249 ATATTTGTATTCTTAGAATTAA
1 ATATTTGCATTCTTAGAATTAA
3386271 GAACAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (22 bp):
ATATTTGCATTCTTAGAATTAA
Found at i:3386436 original size:26 final size:26
Alignment explanation
Indices: 3386407--3386463 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
3386397 TTTTTCAATA
3386407 TACATTCAGTTTTA-CTCTTAGTTTTT
1 TACATT-AGTTTTATCTCTTAGTTTTT
* *
3386433 TACA-TAGTTTTATTTTTTAGTTTTT
1 TACATTAGTTTTATCTCTTAGTTTTT
3386458 TCACAT
1 T-ACAT
3386464 AATATCAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 7 0.27
25 12 0.46
26 7 0.27
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.60
Consensus pattern (26 bp):
TACATTAGTTTTATCTCTTAGTTTTT
Found at i:3386442 original size:24 final size:26
Alignment explanation
Indices: 3386414--3386464 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
3386404 ATATACATTC
3386414 AGTTTTA-CTCTTAGTTTTTT-ACAT
1 AGTTTTATCTCTTAGTTTTTTCACAT
* *
3386438 AGTTTTATTTTTTAGTTTTTTCACAT
1 AGTTTTATCTCTTAGTTTTTTCACAT
3386464 A
1 A
3386465 ATATCAGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 11 0.48
26 5 0.22
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.61
Consensus pattern (26 bp):
AGTTTTATCTCTTAGTTTTTTCACAT
Found at i:3389783 original size:131 final size:129
Alignment explanation
Indices: 3389618--3389858 Score: 385
Period size: 131 Copynumber: 1.9 Consensus size: 129
3389608 TCATAGCATA
* *
3389618 TCACAATAGAAATATGTGATAAATCTTTTGAAAAAAA-TGATGAAGCTCGCATGTAAACCTACAA
1 TCACAATAGAAATATATGATAAATCTTTTAAAAAAAATTGA-GAAGCTCGCATGTAAACCTACAA
* *
3389682 ATACCTCTATAGATCCTAATCATAAACTTGAAGAAGTTTATGATAGATCTATAGGGGTATTTTCA
65 ATACCCCTATAGATCCT-ATCATAAACTTGAAGAAGTTAATGA-AGATCTATAGGGGTATTTTCA
3389747 TC
128 TC
* *
3389749 TCACAATAGAAATATATGATAATTCTTTTAAAAAAAATTGAGAAGCTCGCATGTAAACCTATAAA
1 TCACAATAGAAATATATGATAAATCTTTTAAAAAAAATTGAGAAGCTCGCATGTAAACCTACAAA
*
3389814 TACCCCTATAGATCCTATCATAAACTTGGAGAAGTTAATGAAGAT
66 TACCCCTATAGATCCTATCATAAACTTGAAGAAGTTAATGAAGAT
3389859 GTTACTATAG
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
129 4 0.04
130 23 0.23
131 72 0.71
132 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (129 bp):
TCACAATAGAAATATATGATAAATCTTTTAAAAAAAATTGAGAAGCTCGCATGTAAACCTACAAA
TACCCCTATAGATCCTATCATAAACTTGAAGAAGTTAATGAAGATCTATAGGGGTATTTTCATC
Found at i:3394053 original size:52 final size:52
Alignment explanation
Indices: 3393970--3394072 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 52
3393960 TAAATAAGAA
* *
3393970 GACTTACAGAAGAAAAATTCTAAGAGAAAAAAGATTCTTAATAGACAAGTTC
1 GACTTACAGAAGAAAAATTATAAGAGAAAAAAGATTCTTAACAGACAAGTTC
* * * * *
3394022 GACTTGCAGAAGAATAATTATAAGAGGAAAAATATTCTTAACAGGCAAGTT
1 GACTTACAGAAGAAAAATTATAAGAGAAAAAAGATTCTTAACAGACAAGTT
3394073 TGTATGGTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (52 bp):
GACTTACAGAAGAAAAATTATAAGAGAAAAAAGATTCTTAACAGACAAGTTC
Found at i:3394214 original size:20 final size:20
Alignment explanation
Indices: 3394189--3394234 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3394179 TTACGTCTTA
3394189 TGAGTGTGTATGTTTATTTG
1 TGAGTGTGTATGTTTATTTG
*
3394209 TGAGTGTGTATGTTTGTTTG
1 TGAGTGTGTATGTTTATTTG
3394229 TGAGTG
1 TGAGTG
3394235 GACTAGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (20 bp):
TGAGTGTGTATGTTTATTTG
Found at i:3394339 original size:30 final size:33
Alignment explanation
Indices: 3394282--3394343 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 33
3394272 GTATGGGTGC
3394282 ATATGGGTATGTGTTTGGTTGTATTGAAATGACAT
1 ATATGGGTATGTG-TT-GTTGTATTGAAATGACAT
3394317 ATATGGGTATGTG-T-TTGT-TTGAAATGA
1 ATATGGGTATGTGTTGTTGTATTGAAATGA
3394344 GAATACTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 9 0.33
31 4 0.15
33 1 0.04
35 13 0.48
ACGTcount: A:0.26, C:0.02, G:0.29, T:0.44
Consensus pattern (33 bp):
ATATGGGTATGTGTTGTTGTATTGAAATGACAT
Found at i:3395396 original size:15 final size:16
Alignment explanation
Indices: 3395370--3395399 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3395360 AGAAATGCGA
3395370 GAAAAAATAAGAGATG
1 GAAAAAATAAGAGATG
3395386 GAAAAAA-AAGAGAT
1 GAAAAAATAAGAGAT
3395400 AAGAAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.00, G:0.23, T:0.10
Consensus pattern (16 bp):
GAAAAAATAAGAGATG
Found at i:3395409 original size:17 final size:16
Alignment explanation
Indices: 3395369--3395410 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3395359 AAGAAATGCG
3395369 AGAAAAAATAAGAGAT
1 AGAAAAAATAAGAGAT
*
3395385 GGAAAAAA-AAGAGAT
1 AGAAAAAATAAGAGAT
3395400 AAGAAGAAAAT
1 -AGAA-AAAAT
3395411 TCTGAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 7 0.33
16 10 0.48
17 4 0.19
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (16 bp):
AGAAAAAATAAGAGAT
Found at i:3395617 original size:38 final size:38
Alignment explanation
Indices: 3395546--3395639 Score: 120
Period size: 38 Copynumber: 2.4 Consensus size: 38
3395536 AGATTGGATG
*
3395546 AGGTGCGA-AGGGATTGGGTGTGGTGAGGCGTTGGGGGGA-
1 AGGTG-GAGAGGGATT-GGTGTGGTGAGACGTT-GGGGGAC
* *
3395585 AGGTGGGGAGGGATTGGTGTGGTGAGATGTTGGGGGAC
1 AGGTGGAGAGGGATTGGTGTGGTGAGACGTTGGGGGAC
3395623 AGGTGGAGAGGGATTGG
1 AGGTGGAGAGGGATTGG
3395640 ATAGGGGTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
37 6 0.12
38 31 0.63
39 12 0.24
ACGTcount: A:0.17, C:0.03, G:0.59, T:0.21
Consensus pattern (38 bp):
AGGTGGAGAGGGATTGGTGTGGTGAGACGTTGGGGGAC
Found at i:3396189 original size:26 final size:26
Alignment explanation
Indices: 3396161--3396209 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
3396151 TAAAAAATAA
*
3396161 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
3396186 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
3396210 ATTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:3397678 original size:28 final size:28
Alignment explanation
Indices: 3397632--3397694 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
3397622 TATTTGCAAG
*
3397632 CCATAAAACCATTAACACACAACTAACTT
1 CCAT-AAACCACTAACACACAACTAACTT
* *
3397661 CCATAAACCACTACCACATAACTAACTT
1 CCATAAACCACTAACACACAACTAACTT
3397689 CC-TAAA
1 CCATAAA
3397695 ATTTTGGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 4 0.13
28 23 0.74
29 4 0.13
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (28 bp):
CCATAAACCACTAACACACAACTAACTT
Found at i:3399799 original size:15 final size:16
Alignment explanation
Indices: 3399769--3399801 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3399759 ACCAAATCCC
*
3399769 ATTAATTTATTAAAAG
1 ATTAATTTAGTAAAAG
3399785 ATTAA-TTAGTAAAAG
1 ATTAATTTAGTAAAAG
3399800 AT
1 AT
3399802 AAAGTGACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (16 bp):
ATTAATTTAGTAAAAG
Found at i:3406878 original size:34 final size:34
Alignment explanation
Indices: 3406840--3406909 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
3406830 AATTTTACTT
*
3406840 CTTATTACTTCCTCAATTCTACTCATATTTAACC
1 CTTATTACTGCCTCAATTCTACTCATATTTAACC
3406874 CTTATTACTGCCTCAATTCTACTCATATTTAACC
1 CTTATTACTGCCTCAATTCTACTCATATTTAACC
3406908 CT
1 CT
3406910 CTTTCTACAG
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:0.26, C:0.30, G:0.01, T:0.43
Consensus pattern (34 bp):
CTTATTACTGCCTCAATTCTACTCATATTTAACC
Found at i:3414151 original size:29 final size:29
Alignment explanation
Indices: 3414118--3414176 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3414108 ATTGTGTACC
* * *
3414118 AAATTTGGGGTTTTAAGTTTTGAATTTTA
1 AAATTTAGAGTTTTAAGCTTTGAATTTTA
* *
3414147 AAATTTAGAGTTTTAGGCTTTGGATTTTA
1 AAATTTAGAGTTTTAAGCTTTGAATTTTA
3414176 A
1 A
3414177 GGTTTCAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (29 bp):
AAATTTAGAGTTTTAAGCTTTGAATTTTA
Found at i:3414334 original size:21 final size:21
Alignment explanation
Indices: 3414309--3414358 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
3414299 TATGGTTTGA
*
3414309 AGGGTTTAGGATTTTGATTTT
1 AGGGTTTAGGATTTTAATTTT
*
3414330 AGGGTTTAGGGTTTTAATTTT
1 AGGGTTTAGGATTTTAATTTT
*
3414351 AGGATTTA
1 AGGGTTTA
3414359 AGGTTTAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (21 bp):
AGGGTTTAGGATTTTAATTTT
Found at i:3414351 original size:14 final size:14
Alignment explanation
Indices: 3414334--3414408 Score: 55
Period size: 14 Copynumber: 5.3 Consensus size: 14
3414324 GATTTTAGGG
3414334 TTTAGGGTTTTAAT
1 TTTAGGGTTTTAAT
* *
3414348 TTTA-GGATTTAAGG
1 TTTAGGGTTTTAA-T
*
3414362 TTTAGGGTTTTGA-
1 TTTAGGGTTTTAAT
* *
3414375 TTTATGGGTTTAGAAA
1 TTTA-GGGTTT-TAAT
*
3414391 TTTAGGGTTTCAAT
1 TTTAGGGTTTTAAT
3414405 TTTA
1 TTTA
3414409 AGATTTAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
13 11 0.23
14 20 0.42
15 13 0.27
16 4 0.08
ACGTcount: A:0.24, C:0.01, G:0.24, T:0.51
Consensus pattern (14 bp):
TTTAGGGTTTTAAT
Found at i:3414358 original size:28 final size:28
Alignment explanation
Indices: 3414327--3414415 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
3414317 GGATTTTGAT
3414327 TTTAGGGTTTAGGGTTTTAATTTTAGGA
1 TTTAGGGTTTAGGGTTTTAATTTTAGGA
* * *
3414355 TTTAAGGTTTAGGGTTTTGA-TTTATGGG
1 TTTAGGGTTTAGGGTTTTAATTTTA-GGA
** * *
3414383 TTTAGAAATTTAGGGTTTCAATTTTAAGA
1 TTTAG-GGTTTAGGGTTTTAATTTTAGGA
3414412 TTTA
1 TTTA
3414416 AAAATTTAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
27 4 0.08
28 24 0.50
29 16 0.33
30 4 0.08
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (28 bp):
TTTAGGGTTTAGGGTTTTAATTTTAGGA
Found at i:3414363 original size:21 final size:21
Alignment explanation
Indices: 3414320--3414364 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3414310 GGGTTTAGGA
* * *
3414320 TTTTGATTTTAGGGTTTAGGG
1 TTTTAATTTTAGGATTTAAGG
3414341 TTTTAATTTTAGGATTTAAGG
1 TTTTAATTTTAGGATTTAAGG
3414362 TTT
1 TTT
3414365 AGGGTTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (21 bp):
TTTTAATTTTAGGATTTAAGG
Found at i:3414385 original size:79 final size:77
Alignment explanation
Indices: 3414200--3414386 Score: 175
Period size: 79 Copynumber: 2.4 Consensus size: 77
3414190 TAAGGTTCGA
**
3414200 AAGGTTTAGAGGTTTTGATTCTA-GCATTTAAAGGGTTAAGGTTTCGATTTTAGGGTTTGGAGTT
1 AAGGTTTAG-GGTTTTGATT-TATGGGTTTAAAGGGTTAAGGTTTCGATTTTAGGGTTTGGAGTT
*
3414264 TAGGGTTTTGAATTT
64 TA-GATTTTGAATTT
* ** * * * *
3414279 ATGGTTTAAAGTTTTAGTTTTAT-GGTTTGAAGGGTTTAGGATTTTGATTTTAGGGTTTAGG-GT
1 AAGGTTTAGGGTTTT-GATTTATGGGTTTAAAGGGTTAAGG-TTTCGATTTTAGGGTTT-GGAG-
*
3414342 TTTA-ATTTTAGGATTT
62 TTTAGATTTT-GAATTT
3414358 AAGGTTTAGGGTTTTGATTTATGGGTTTA
1 AAGGTTTAGGGTTTTGATTTATGGGTTTA
3414387 GAAATTTAGG
Statistics
Matches: 85, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
78 30 0.35
79 49 0.58
80 6 0.07
ACGTcount: A:0.22, C:0.02, G:0.28, T:0.48
Consensus pattern (77 bp):
AAGGTTTAGGGTTTTGATTTATGGGTTTAAAGGGTTAAGGTTTCGATTTTAGGGTTTGGAGTTTA
GATTTTGAATTT
Found at i:3414415 original size:29 final size:28
Alignment explanation
Indices: 3414334--3414447 Score: 104
Period size: 29 Copynumber: 4.0 Consensus size: 28
3414324 GATTTTAGGG
**
3414334 TTTAGGGTTTTAATTTTAGGATTTAAGG
1 TTTAGGGTTTTAATTTTAGGATTTAAAA
* *
3414362 TTTAGGGTTTTGA-TTTATGGGTTTAGAAA
1 TTTAGGGTTTTAATTTTA-GGATTTA-AAA
* *
3414391 TTTAGGGTTTCAATTTTAAGATTTAAAAA
1 TTTAGGGTTTTAATTTTAGGATTT-AAAA
* ** *
3414420 TTTAGGATTTGGATTTTAGGGTTTAAAA
1 TTTAGGGTTTTAATTTTAGGATTTAAAA
3414448 AAAATCTGAA
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
27 4 0.06
28 22 0.32
29 38 0.55
30 5 0.07
ACGTcount: A:0.29, C:0.01, G:0.23, T:0.47
Consensus pattern (28 bp):
TTTAGGGTTTTAATTTTAGGATTTAAAA
Found at i:3414733 original size:3 final size:3
Alignment explanation
Indices: 3414725--3414760 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3414715 TTTTATATAT
3414725 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3414761 AAGGTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3414942 original size:22 final size:23
Alignment explanation
Indices: 3414910--3414971 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
3414900 TATCATGCAT
*
3414910 AAATATTAAAAATAA-AACTA-AA
1 AAATATCAAAAATAATAA-TATAA
3414932 AAATATCAAAAATAATAATATAA
1 AAATATCAAAAATAATAATATAA
*
3414955 AAAAATTCAAAAATAAT
1 AAATA-TCAAAAATAAT
3414972 TCAAAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 16 0.46
23 8 0.23
24 11 0.31
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (23 bp):
AAATATCAAAAATAATAATATAA
Found at i:3414972 original size:11 final size:11
Alignment explanation
Indices: 3414953--3414981 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3414943 ATAATAATAT
3414953 AAAAA-AATTC
1 AAAAATAATTC
3414963 AAAAATAATTC
1 AAAAATAATTC
3414974 AAAAATAA
1 AAAAATAA
3414982 AAAATTAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAATAATTC
Found at i:3416106 original size:12 final size:13
Alignment explanation
Indices: 3416082--3416120 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
3416072 ATCACTGTTC
3416082 TTTTT-TTTATTA
1 TTTTTATTTATTA
3416094 TTTTTATTT-TTA
1 TTTTTATTTATTA
*
3416106 TTTTTATTAATTA
1 TTTTTATTTATTA
3416119 TT
1 TT
3416121 ATATTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTATTTATTA
Found at i:3416125 original size:24 final size:21
Alignment explanation
Indices: 3416085--3416130 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 21
3416075 ACTGTTCTTT
3416085 TTTTTATTATTTTTATTTTTA
1 TTTTTATTATTTTTATTTTTA
3416106 TTTTTATTAATTATTATATTTTTA
1 TTTTTATT-ATT-TT-TATTTTTA
3416130 T
1 T
3416131 AATAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.36
22 3 0.14
23 2 0.09
24 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTATTATTTTTATTTTTA
Found at i:3416693 original size:19 final size:15
Alignment explanation
Indices: 3416652--3416681 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3416642 CTTCATTTGA
3416652 AATTTATTGATTCAT
1 AATTTATTGATTCAT
3416667 AATTTATTGATTCAT
1 AATTTATTGATTCAT
3416682 TAAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
AATTTATTGATTCAT
Found at i:3417052 original size:32 final size:31
Alignment explanation
Indices: 3417016--3417083 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 31
3417006 ACTTATTTAC
*
3417016 TTTATTTTTTATAATAA-ATTAAATCTATTTGT
1 TTTATTATTTATAATAAGA-TAAATCTATTT-T
*
3417048 TTTATTATTTATAATAAGATAAATTTATTTT
1 TTTATTATTTATAATAAGATAAATCTATTTT
3417079 TTTAT
1 TTTAT
3417084 ACAAAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 6 0.18
32 26 0.79
33 1 0.03
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.60
Consensus pattern (31 bp):
TTTATTATTTATAATAAGATAAATCTATTTT
Found at i:3428485 original size:109 final size:109
Alignment explanation
Indices: 3428356--3428570 Score: 394
Period size: 109 Copynumber: 2.0 Consensus size: 109
3428346 AAATATAAGC
* *
3428356 GGATGATATGATAATAAAAAAATTAGAGCTTGATTGAGCACCTAGATAAGATTTTGGCTCTTTTT
1 GGATGATATGATAATAAAAAAATTAGAGCTTGATTAAGCACCTAGATAAGATTTTGGCTCTTCTT
*
3428421 TTAATCCTCGTAGCGGGTTCTGCCTACCTAAACCAATTAAAAGT
66 TTAATCCTCGTAACGGGTTCTGCCTACCTAAACCAATTAAAAGT
3428465 GGATGATATGATAATAAAAAAATTAGAGCTTGATTAAGCACCTAGATAAGATTTTGGCTCTTCTT
1 GGATGATATGATAATAAAAAAATTAGAGCTTGATTAAGCACCTAGATAAGATTTTGGCTCTTCTT
*
3428530 TTAATCCTCGTAACGGGTTCTGCCTTCCTAAACCAATTAAA
66 TTAATCCTCGTAACGGGTTCTGCCTACCTAAACCAATTAAA
3428571 TTTGTACATT
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 102 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (109 bp):
GGATGATATGATAATAAAAAAATTAGAGCTTGATTAAGCACCTAGATAAGATTTTGGCTCTTCTT
TTAATCCTCGTAACGGGTTCTGCCTACCTAAACCAATTAAAAGT
Found at i:3428659 original size:22 final size:20
Alignment explanation
Indices: 3428620--3428659 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
3428610 ACTTCCATGG
3428620 ATTATAATAATATCTTAACC
1 ATTATAATAATATCTTAACC
*
3428640 ATTATCAATTAATATTTTAA
1 ATTAT-AA-TAATATCTTAA
3428660 TAATCCTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTATAATAATATCTTAACC
Found at i:3430881 original size:25 final size:25
Alignment explanation
Indices: 3430844--3430908 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
3430834 ATATTTTTAT
**
3430844 TATTTTTATTTTATATTTTATGTATA
1 TATTTTTA-TTTATATCCTATGTATA
* *
3430870 TATTTTTCTTTATATCCTATGTATT
1 TATTTTTATTTATATCCTATGTATA
3430895 TATTATTTATTTAT
1 TATT-TTTATTTAT
3430909 TATTACTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 18 0.55
26 15 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (25 bp):
TATTTTTATTTATATCCTATGTATA
Found at i:3430883 original size:14 final size:14
Alignment explanation
Indices: 3430839--3430884 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
3430829 GTTTTATATT
3430839 TTTAT-TATTTTTA
1 TTTATATATTTTTA
3430852 TTT-TATA-TTTTA
1 TTTATATATTTTTA
* *
3430864 TGTATATATTTTTC
1 TTTATATATTTTTA
3430878 TTTATAT
1 TTTATAT
3430885 CCTATGTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
12 8 0.30
13 9 0.33
14 10 0.37
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTATATATTTTTA
Found at i:3431027 original size:34 final size:33
Alignment explanation
Indices: 3430925--3431027 Score: 88
Period size: 34 Copynumber: 3.1 Consensus size: 33
3430915 TATTTATTAA
*
3430925 TATTTTTTTCT-TTTTTTTTTTAT-TTT-ATAT
1 TATTTTTTTCTATTTTTTATTTATCTTTAATAT
* ** * *
3430955 GTATTTTTATT-TATCTCATATTTATCTGTTATTTT
1 -TATTTTT-TTCTATTTTTTATTTATCT-TTAATAT
3430990 TATTTTTTTCTATTTTTTATTTATCTTATAATAT
1 TATTTTTTTCTATTTTTTATTTATCTT-TAATAT
3431024 TATT
1 TATT
3431028 GTTGATTTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
31 8 0.15
32 10 0.19
33 4 0.07
34 30 0.56
35 2 0.04
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (33 bp):
TATTTTTTTCTATTTTTTATTTATCTTTAATAT
Found at i:3431052 original size:45 final size:44
Alignment explanation
Indices: 3430943--3431052 Score: 100
Period size: 45 Copynumber: 2.5 Consensus size: 44
3430933 TCTTTTTTTT
* *
3430943 TTTATTTTA-TATGTATTTTTATTTATCTCATATTTATCTGTTA
1 TTTATATTATTATCTATTTTTATTTATCTCATATTTATCTGTTA
* * * *
3430986 TTTTTATTTTTTTCTATTTTTTATTTATCTTATAATATTAT-TGTTGA
1 TTTATATTATTATCTA-TTTTTATTTATCTCAT-AT-TTATCTGTT-A
*
3431033 TTTATCTTATTAT-TATTTTT
1 TTTATATTATTATCTATTTTT
3431053 CTAATTATCT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
43 6 0.12
44 4 0.08
45 20 0.38
46 8 0.15
47 14 0.27
ACGTcount: A:0.22, C:0.05, G:0.04, T:0.69
Consensus pattern (44 bp):
TTTATATTATTATCTATTTTTATTTATCTCATATTTATCTGTTA
Found at i:3432004 original size:26 final size:25
Alignment explanation
Indices: 3431975--3432046 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 25
3431965 TTTATCTTTA
*
3431975 TTTTATTTTTATTTTTGGTTTTACTT-
1 TTTTATTTTTATTTTT-ATTTT-CTTC
3432001 TTTTATTTTTATTTTTATTTTCTTC
1 TTTTATTTTTATTTTTATTTTCTTC
3432026 TTTTACTTTATTA-TTTTATTT
1 TTTTA-TTT-TTATTTTTATTT
3432047 CCTTTTTAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
24 3 0.07
25 9 0.21
26 27 0.64
27 3 0.07
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.78
Consensus pattern (25 bp):
TTTTATTTTTATTTTTATTTTCTTC
Found at i:3432011 original size:32 final size:32
Alignment explanation
Indices: 3431971--3432046 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
3431961 TTCTTTTATC
*
3431971 TTTATTTTATTTTTATTTT-TGGTTTTACTTT
1 TTTATTTTATTTTTATTTTCTGCTTTTACTTT
*
3432002 TTTATTTTTATTTTTATTTTCTTCTTTTACTTT
1 TTTA-TTTTATTTTTATTTTCTGCTTTTACTTT
*
3432035 ATTATTTTATTT
1 TTTATTTTATTT
3432047 CCTTTTTAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 4 0.10
32 23 0.57
33 13 0.32
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (32 bp):
TTTATTTTATTTTTATTTTCTGCTTTTACTTT
Found at i:3432034 original size:6 final size:6
Alignment explanation
Indices: 3431964--3432021 Score: 64
Period size: 6 Copynumber: 9.5 Consensus size: 6
3431954 TTTAATGTTC
* **
3431964 TTTTAT CTTTA- TTTTAT TTTTAT TTTTGG TTTTACTT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA--T TTTTAT TTTTAT
3432013 TTTTAT TTT
1 TTTTAT TTT
3432022 CTTCTTTTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 4 0.09
6 34 0.79
8 5 0.12
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:3432188 original size:117 final size:116
Alignment explanation
Indices: 3432068--3432532 Score: 731
Period size: 117 Copynumber: 4.0 Consensus size: 116
3432058 AAAATCTAAA
* * * *
3432068 AAAAAATAAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTGTTAATTTTTCTTAAAAAT
1 AAAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT
3432133 AAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTT
66 AAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTT
3432184 AAAAAATTAAAATTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTTTAAA
1 AAAAAA-TAAAATTTC-AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTAAA
3432248 AATAAATCTTCAAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTT
63 AATAAATCTTCAAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTT
* * *
3432303 TAAAAATAAAATTTCAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 AAAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT
*
3432368 AAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAAATTTTCTT
66 AAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATC-AATTTTCTT
*
3432420 -AAAAAT-AAATCTTCAAGAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTTCTTAAAA
1 AAAAAATAAAAT-TTCAA-AAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAA
* * *
3432483 ATAAATTTTC-AAAAGATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTC
64 ATAAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
3432533 CCTACACAAA
Statistics
Matches: 326, Mismatches: 15, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
115 11 0.03
116 74 0.23
117 131 0.40
118 68 0.21
119 42 0.13
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (116 bp):
AAAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT
AAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTT
Found at i:3432264 original size:59 final size:58
Alignment explanation
Indices: 3432069--3432532 Score: 697
Period size: 58 Copynumber: 7.9 Consensus size: 58
3432059 AAATCTAAAA
* * * *
3432069 AAAAATAAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTGTTAATTTT-TCTT
1 AAAAATAAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCT-TT
*
3432127 AAAAATAAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTA
1 AAAAATAAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTT
3432185 AAAAATTAAAAT-TTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTT
1 AAAAA-T-AAATCTTC-AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTT
3432245 AAAAATAAATCTTCAAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTT
1 AAAAATAAATCTTCAAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTT
* *
3432304 AAAAATAAAAT-TTCAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAAT-AAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTT
*
3432362 AAAAATAAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAAATTTTC-TT
1 AAAAATAAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATC-AATTTTCTTT
*
3432420 AAAAATAAATCTTCAAGAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTT-TCTT
1 AAAAATAAATCTTCAA-AAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCT-TT
* * *
3432479 AAAAATAAATTTTC-AAAAGATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTC
1 AAAAATAAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
3432533 CCTACACAAA
Statistics
Matches: 379, Mismatches: 14, Indels: 26
0.90 0.03 0.06
Matches are distributed among these distances:
57 39 0.10
58 168 0.44
59 116 0.31
60 56 0.15
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (58 bp):
AAAAATAAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTT
Found at i:3436651 original size:27 final size:27
Alignment explanation
Indices: 3436563--3436651 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
3436553 TCTTTTAAGG
3436563 AAAATTGATACTTTCAACTTTTCCCTA
1 AAAATTGATACTTTCAACTTTTCCCTA
** * * * *
3436590 AAAA-T-ATTTTTTGGAAATTTATTCTTAA
1 AAAATTGATACTTT-CAACTTT-TCCCT-A
3436618 GGAAAATTGATACTTTCAACTTTTCCCTA
1 --AAAATTGATACTTTCAACTTTTCCCTA
3436647 AAAAT
1 AAAAT
3436652 ATATTTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 14
0.62 0.17 0.20
Matches are distributed among these distances:
25 5 0.12
26 6 0.14
27 12 0.28
28 1 0.02
29 1 0.02
30 7 0.16
31 6 0.14
32 5 0.12
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTCCCTA
Found at i:3436721 original size:60 final size:59
Alignment explanation
Indices: 3436370--3436734 Score: 443
Period size: 60 Copynumber: 6.1 Consensus size: 59
3436360 AATGATTTTT
* *
3436370 TTTTTAGGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGGAAATTTTGA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAA-TTT-A
* * ***
3436430 TTTTAAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAA-CCCTTTTTTTGAAAATTTA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTG-AAATTTA
* *
3436489 TTTCTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGGAAATTTA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTT-GAAATTTA
* *
3436549 TTTTTCTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTGGAAATTTA
1 ----T-TTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAATTTA
* *
3436611 TTCTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTTGAAATTTA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTTTTTGAAATTTA
* * *
3436671 TTTTTGAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATTATTTTTTTTTTGAAATTT-
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TA-TTTTTTTTTGAAATTTA
3436731 TTTT
1 TTTT
3436735 ATTTTTATCT
Statistics
Matches: 267, Mismatches: 24, Indels: 28
0.84 0.08 0.09
Matches are distributed among these distances:
57 40 0.15
58 1 0.00
59 37 0.14
60 114 0.43
61 21 0.08
62 9 0.03
63 6 0.02
64 1 0.00
65 38 0.14
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (59 bp):
TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAATTTA
Found at i:3436728 original size:17 final size:17
Alignment explanation
Indices: 3436708--3436740 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3436698 TTTTTCTCAA
3436708 AAATTATTTTT-TTTTTG
1 AAATT-TTTTTATTTTTG
3436725 AAATTTTTTTATTTTT
1 AAATTTTTTTATTTTT
3436741 ATCTAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
AAATTTTTTTATTTTTG
Found at i:3436828 original size:20 final size:19
Alignment explanation
Indices: 3436803--3436854 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
3436793 CTAATCTAAT
*
3436803 AAATAAAAAATAAAATAAAC
1 AAATAAAAAA-AAAATAAAA
*
3436823 AAATAAACAAAGAAATAAAA
1 AAATAAA-AAAAAAATAAAA
3436843 AAATAAAAAAAA
1 AAATAAAAAAAA
3436855 TTCAAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 21 0.75
21 3 0.11
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.12
Consensus pattern (19 bp):
AAATAAAAAAAAAATAAAA
Found at i:3436846 original size:8 final size:8
Alignment explanation
Indices: 3436803--3436853 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
3436793 CTAATCTAAT
3436803 AAAT-AAA
1 AAATAAAA
3436810 AAATAAAA
1 AAATAAAA
* *
3436818 TAAACAAAT
1 -AAATAAAA
* *
3436827 AAACAAAG
1 AAATAAAA
3436835 AAATAAAA
1 AAATAAAA
3436843 AAATAAAA
1 AAATAAAA
3436851 AAA
1 AAA
3436854 ATTCAAAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
7 4 0.11
8 27 0.73
9 6 0.16
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:3436860 original size:27 final size:28
Alignment explanation
Indices: 3436830--3436882 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
3436820 AACAAATAAA
* *
3436830 CAAAGAAATAAA-AAAATAAAAAAAATT
1 CAAAGAAAGAAAGAAAAAAAAAAAAATT
3436857 CAAAGAAAGAAAGAAAAAAAAAAAAA
1 CAAAGAAAGAAAGAAAAAAAAAAAAA
3436883 AAACCTGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.81, C:0.04, G:0.08, T:0.08
Consensus pattern (28 bp):
CAAAGAAAGAAAGAAAAAAAAAAAAATT
Found at i:3438548 original size:10 final size:10
Alignment explanation
Indices: 3438533--3438571 Score: 60
Period size: 10 Copynumber: 3.7 Consensus size: 10
3438523 AAAAGATGAT
3438533 GAAAAAAAAA
1 GAAAAAAAAA
3438543 GAAAAAAAAA
1 GAAAAAAAAA
3438553 GAAAAAAAGAA
1 GAAAAAAA-AA
3438564 GGAAAAAA
1 -GAAAAAA
3438572 TGAGAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.67
11 2 0.07
12 7 0.26
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:3438577 original size:22 final size:20
Alignment explanation
Indices: 3438517--3438579 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
3438507 GAAAAATGAG
*
3438517 AAAAAA-AAAAGATGATGAAA
1 AAAAAAGAAAAAATGA-GAAA
**
3438537 AAAAAAGAAAAAAAAAGAAA
1 AAAAAAGAAAAAATGAGAAA
3438557 AAAAGAAGGAAAAAATGAGAAA
1 AAAA-AA-GAAAAAATGAGAAA
3438579 A
1 A
3438580 TGAAAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 14 0.40
21 8 0.23
22 13 0.37
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAAAAGAAAAAATGAGAAA
Found at i:3438589 original size:20 final size:19
Alignment explanation
Indices: 3438536--3438589 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
3438526 AGATGATGAA
3438536 AAAAAAAG-AAAAAAAAAG
1 AAAAAAAGAAAAAAAAAAG
* *
3438554 AAAAAAAGAAGGAAAAAATG
1 AAAAAAAGAA-AAAAAAAAG
* *
3438574 AGAAAATGAAAAAAAA
1 AAAAAAAGAAAAAAAA
3438590 GATTCAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 8 0.28
19 6 0.21
20 15 0.52
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAAAAG
Found at i:3439877 original size:41 final size:41
Alignment explanation
Indices: 3439832--3440377 Score: 716
Period size: 41 Copynumber: 13.1 Consensus size: 41
3439822 ATGATTGTCA
*
3439832 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTCTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
3439873 AGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
*
3439915 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * *
3439956 AGGAGCAATTTACTTTCCAAAAATCGTGGTGCCTCTGTGTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
* * * *
3439998 ATGAGCAATTTACTTTTTAAAGTCATGGTGCCTTTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
3440039 AGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
* * *
3440081 AGGAGCAATTTATTTTTCAAAGTCCTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
3440122 AGGAGCAATTTACTTTACAAAAGTCGTGGTGCCTTTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
*
3440164 ATGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
3440205 AGGAGCAATTTA-TTTTCCAAAAGTCATGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTT-C-AAAGTCGTGGTGCCTCTGTTTAG
*
3440247 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * ** * *
3440288 AGGAGCAATTTATTTTTCAAAGTCGTTGAACCTTTGATTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * * * *
3440329 AGGAGCCATTTATGTTTCTCAAAGTCGTTGAGTCTCTGCTTAG
1 AGGAGCAATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAG
3440372 AGGAGC
1 AGGAGC
3440378 TTTGGTAAAA
Statistics
Matches: 444, Mismatches: 52, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
40 4 0.01
41 226 0.51
42 184 0.41
43 30 0.07
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:3439971 original size:83 final size:83
Alignment explanation
Indices: 3439832--3440377 Score: 772
Period size: 83 Copynumber: 6.6 Consensus size: 83
3439822 ATGATTGTCA
* *
3439832 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTCTTTAGAGGAGCAATTTACTTTCCAAAAGT
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGT
*
3439897 CGTGGTGCCTCTATTTAG
66 CGTGGTGCCTCTGTTTAG
*
3439915 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAAT
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGT
*
3439980 CGTGGTGCCTCTGTGTAG
66 CGTGGTGCCTCTGTTTAG
* * *
3439998 ATGAGCAATTTACTTTTT-AAAGTCATGGTGCCTTTGTTTAGAGGAGCAATTTACTTTCCAAAAG
1 AGGAGCAATTTA-TTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAG
3440062 TCGTGGTGCCTCTGTTTAG
65 TCGTGGTGCCTCTGTTTAG
* * *
3440081 AGGAGCAATTTATTTTTCAAAGTCCTGGTGCCTCTATTTAGAGGAGCAATTTACTTTACAAAAGT
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGT
*
3440146 CGTGGTGCCTTTGTTTAG
66 CGTGGTGCCTCTGTTTAG
* * *
3440164 ATGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAAGT
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGT
* *
3440229 CATGGTACCTCTGTTTAG
66 CGTGGTGCCTCTGTTTAG
* * * *
3440247 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTC-AAAGT
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGT
* ** * *
3440311 CGTTGAACCTTTGATTAG
66 CGTGGTGCCTCTGTTTAG
* * * * *
3440329 AGGAGCCATTTATGTTTCTCAAAGTCGTTGAGTCTCTGCTTAGAGGAGC
1 AGGAGCAATTTAT-TTT-TCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
3440378 TTTGGTAAAA
Statistics
Matches: 419, Mismatches: 40, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
82 34 0.08
83 354 0.84
84 31 0.07
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (83 bp):
AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGT
CGTGGTGCCTCTGTTTAG
Found at i:3440405 original size:15 final size:14
Alignment explanation
Indices: 3440384--3440428 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
3440374 GAGCTTTGGT
3440384 AAAAAAAAAATAAA
1 AAAAAAAAAATAAA
*
3440398 ACAAAAAAAATAAA
1 AAAAAAAAAATAAA
3440412 AAAACAAAAAATGAAA
1 AAAA-AAAAAAT-AAA
3440428 A
1 A
3440429 TGTTGAGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 16 0.59
15 7 0.26
16 4 0.15
ACGTcount: A:0.87, C:0.04, G:0.02, T:0.07
Consensus pattern (14 bp):
AAAAAAAAAATAAA
Found at i:3440406 original size:17 final size:17
Alignment explanation
Indices: 3440384--3440422 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3440374 GAGCTTTGGT
*
3440384 AAAAAAAA-AATAAAAC
1 AAAAAAAATAAAAAAAC
3440400 AAAAAAAATAAAAAAAC
1 AAAAAAAATAAAAAAAC
3440417 AAAAAA
1 AAAAAA
3440423 TGAAAATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.90, C:0.05, G:0.00, T:0.05
Consensus pattern (17 bp):
AAAAAAAATAAAAAAAC
Found at i:3440605 original size:13 final size:12
Alignment explanation
Indices: 3440569--3440620 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
3440559 GGTAAGCTCA
3440569 ATTTTATTTTAT
1 ATTTTATTTTAT
*
3440581 ATTTT-TGTTAT
1 ATTTTATTTTAT
3440592 -TTTTATTTTAT
1 ATTTTATTTTAT
*
3440603 ATTTTATGTATAT
1 ATTTTAT-TTTAT
3440616 ATTTT
1 ATTTT
3440621 CCTTTATATC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 4 0.12
11 10 0.29
12 11 0.32
13 9 0.26
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (12 bp):
ATTTTATTTTAT
Found at i:3440626 original size:25 final size:25
Alignment explanation
Indices: 3440569--3440643 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 25
3440559 GGTAAGCTCA
*
3440569 ATTTTATTTTATATTTT-TGT-TAT
1 ATTTTACTTTATATTTTATGTATAT
*
3440592 -TTTTATTTTATATTTTATGTATAT
1 ATTTTACTTTATATTTTATGTATAT
* ** *
3440616 ATTTTCCTTTATATCCTATGTATTT
1 ATTTTACTTTATATTTTATGTATAT
3440641 ATT
1 ATT
3440644 AGTTATTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 16 0.36
23 3 0.07
24 3 0.07
25 22 0.50
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (25 bp):
ATTTTACTTTATATTTTATGTATAT
Done.