Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 156 of 297
Found at i:53170994 original size:5 final size:5
Alignment explanation
Indices: 53170979--53171029 Score: 50
Period size: 5 Copynumber: 10.4 Consensus size: 5
53170969 TTTTCTATAT
* * * * *
53170979 ATTTA AATTA ATTTA ATTTA AATTA AATTA ATTAA ATTT- ATATA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
53171028 AT
1 AT
53171030 GTTTATTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
4 3 0.08
5 34 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (5 bp):
ATTTA
Found at i:53170999 original size:15 final size:15
Alignment explanation
Indices: 53170979--53171028 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
53170969 TTTTCTATAT
53170979 ATTTAAATTAATTTA
1 ATTTAAATTAATTTA
*
53170994 ATTTAAATTAAATTA
1 ATTTAAATTAATTTA
* *
53171009 A-TTAAATTTATATA
1 ATTTAAATTAATTTA
53171023 ATTTAA
1 ATTTAA
53171029 TGTTTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAAATTAATTTA
Found at i:53171006 original size:20 final size:20
Alignment explanation
Indices: 53170981--53171018 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53170971 TTCTATATAT
*
53170981 TTAAATTAATTTAATTTAAA
1 TTAAATTAATTAAATTTAAA
53171001 TTAAATTAATTAAATTTA
1 TTAAATTAATTAAATTTA
53171019 TATAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAATTAATTAAATTTAAA
Found at i:53188468 original size:1 final size:1
Alignment explanation
Indices: 53188462--53188506 Score: 63
Period size: 1 Copynumber: 45.0 Consensus size: 1
53188452 CTAGATATAC
* * *
53188462 AAAAAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
53188507 GAAACTCGTC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:53189495 original size:63 final size:63
Alignment explanation
Indices: 53189396--53189521 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
53189386 TGTGGTTTAA
53189396 GTCTGATAAGTTGCGAGGCCAATGGTGCTTGGTTGATGTGGGCACTATAGAAATGGTTCTTTG
1 GTCTGATAAGTTGCGAGGCCAATGGTGCTTGGTTGATGTGGGCACTATAGAAATGGTTCTTTG
53189459 GTCTGATAAGTTGCGAGGCCAATGGTGCTTGGTTGATGTGGGCACTATAGAAATGGTTCTTTG
1 GTCTGATAAGTTGCGAGGCCAATGGTGCTTGGTTGATGTGGGCACTATAGAAATGGTTCTTTG
53189522 TGTAGTAGGC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.21, C:0.13, G:0.33, T:0.33
Consensus pattern (63 bp):
GTCTGATAAGTTGCGAGGCCAATGGTGCTTGGTTGATGTGGGCACTATAGAAATGGTTCTTTG
Found at i:53189514 original size:31 final size:31
Alignment explanation
Indices: 53189416--53189515 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 31
53189406 TTGCGAGGCC
53189416 AATGGTGCTTGGTTGATGTGGGCACTATAGA
1 AATGGTGCTTGGTTGATGTGGGCACTATAGA
* * * * *
53189447 AATGGTTCTTTGGTCTGATAAGT-TG--CGA-GGCC
1 AATGGTGC-TTGGT-TGAT--GTGGGCACTATAG-A
53189479 AATGGTGCTTGGTTGATGTGGGCACTATAGA
1 AATGGTGCTTGGTTGATGTGGGCACTATAGA
53189510 AATGGT
1 AATGGT
53189516 TCTTTGTGTA
Statistics
Matches: 50, Mismatches: 10, Indels: 18
0.64 0.13 0.23
Matches are distributed among these distances:
28 2 0.04
29 1 0.02
30 4 0.08
31 21 0.42
32 15 0.30
33 4 0.08
34 1 0.02
35 2 0.04
ACGTcount: A:0.22, C:0.11, G:0.34, T:0.33
Consensus pattern (31 bp):
AATGGTGCTTGGTTGATGTGGGCACTATAGA
Found at i:53196159 original size:32 final size:33
Alignment explanation
Indices: 53196112--53196190 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
53196102 ATATATTATA
*
53196112 TATATTATGTATATATT-TTTAATGT-TATTAGTTG
1 TATATTATCT-TATATTATTTAATGTATA-TA-TTG
* *
53196146 TATATT-TCTTATATTATTTCATGTATATATTT
1 TATATTATCTTATATTATTTAATGTATATATTG
53196178 TATATTATCTTAT
1 TATATTATCTTAT
53196191 GTACATATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
32 14 0.36
33 17 0.44
34 8 0.21
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (33 bp):
TATATTATCTTATATTATTTAATGTATATATTG
Found at i:53196192 original size:23 final size:23
Alignment explanation
Indices: 53196101--53196199 Score: 82
Period size: 23 Copynumber: 4.3 Consensus size: 23
53196091 GTATATATTG
*
53196101 TATATATTATA-TATATTATGTA
1 TATATTTTATATTATATTATGTA
53196123 TATATTTT-TAATGT-TATTAGTTGTA
1 TATATTTTAT-AT-TATATTA--TGTA
53196148 TAT-TTCTTATATTAT-TTCATGTA
1 TATATT-TTATATTATATT-ATGTA
*
53196171 TATATTTTATATTATCTTATGTA
1 TATATTTTATATTATATTATGTA
*
53196194 CATATT
1 TATATT
53196200 CTGAAATACT
Statistics
Matches: 64, Mismatches: 2, Indels: 21
0.74 0.02 0.24
Matches are distributed among these distances:
21 1 0.02
22 8 0.12
23 31 0.48
24 10 0.16
25 13 0.20
26 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (23 bp):
TATATTTTATATTATATTATGTA
Found at i:53196342 original size:17 final size:19
Alignment explanation
Indices: 53196320--53196355 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
53196310 TTTACTATAC
53196320 GTGTATATA-TA-TATTTT
1 GTGTATATAGTATTATTTT
53196337 GTGTATATAGTATTATTTT
1 GTGTATATAGTATTATTTT
53196356 CGTATATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 2 0.12
19 6 0.35
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (19 bp):
GTGTATATAGTATTATTTT
Found at i:53196362 original size:18 final size:17
Alignment explanation
Indices: 53196322--53196372 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
53196312 TACTATACGT
*
53196322 GTATATATATATTTTGT
1 GTATATATATATTTTGC
53196339 GTATATAGTATTATTTT-C
1 GTATATA-TA-TATTTTGC
53196357 GTATATCATTATATTT
1 GTATAT-A-TATATTT
53196373 ATCATTATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 7 0.24
18 13 0.45
19 9 0.31
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (17 bp):
GTATATATATATTTTGC
Found at i:53208048 original size:2 final size:2
Alignment explanation
Indices: 53208041--53208080 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
53208031 TAAACAATAA
53208041 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
53208081 ATGTCCAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:53209445 original size:6 final size:6
Alignment explanation
Indices: 53209434--53209460 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53209424 TTTTATTGTG
53209434 GAAGGA GAAGGA GAAGGA GAAGGA GAA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAA
53209461 AAATATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:53212494 original size:19 final size:18
Alignment explanation
Indices: 53212467--53212503 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
53212457 AATATATATA
53212467 TTTTTAACCCAAACTTTT
1 TTTTTAACCCAAACTTTT
*
53212485 TTTTTGAACCCCAACTTTT
1 TTTTT-AACCCAAACTTTT
53212504 GTAAGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.24, C:0.24, G:0.03, T:0.49
Consensus pattern (18 bp):
TTTTTAACCCAAACTTTT
Found at i:53213826 original size:29 final size:29
Alignment explanation
Indices: 53213744--53213825 Score: 101
Period size: 31 Copynumber: 2.7 Consensus size: 29
53213734 AAATCTCAAA
* * *
53213744 TCTATACATGAACTTTGGTCTAATGTTCAAT
1 TCTATACATGAACTTTGAT-T-TTGTGCAAT
53213775 TCTATACATGAACTTTGATTTTGTGCAAT
1 TCTATACATGAACTTTGATTTTGTGCAAT
*
53213804 TTTATACATGAAACTTTGATTT
1 TCTATACATG-AACTTTGATTT
53213826 GATCCAATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 16 0.35
30 12 0.26
31 18 0.39
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.45
Consensus pattern (29 bp):
TCTATACATGAACTTTGATTTTGTGCAAT
Found at i:53213834 original size:30 final size:29
Alignment explanation
Indices: 53213744--53213836 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 29
53213734 AAATCTCAAA
* * *
53213744 TCTATACATGAACTTTGGTCTAATGTTCAAT
1 TCTATACATGAACTTTGAT-T-TTGTCCAAT
*
53213775 TCTATACATGAACTTTGATTTTGTGCAAT
1 TCTATACATGAACTTTGATTTTGTCCAAT
*
53213804 TTTATACATGAAACTTTGA-TTTGATCCAAT
1 TCTATACATG-AACTTTGATTTTG-TCCAAT
53213834 TCT
1 TCT
53213837 CACAAATTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
29 20 0.37
30 16 0.30
31 18 0.33
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (29 bp):
TCTATACATGAACTTTGATTTTGTCCAAT
Found at i:53220855 original size:21 final size:23
Alignment explanation
Indices: 53220815--53220856 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
53220805 GGTTATTAGA
53220815 ATTTTACAAATTAAAAAATATTT
1 ATTTTACAAATTAAAAAATATTT
*
53220838 ATTTTA-AAA-TAAATAATAT
1 ATTTTACAAATTAAAAAATAT
53220857 AAAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 3 0.17
23 6 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTTACAAATTAAAAAATATTT
Found at i:53238988 original size:18 final size:18
Alignment explanation
Indices: 53238969--53239097 Score: 159
Period size: 18 Copynumber: 7.2 Consensus size: 18
53238959 CCCAACTACT
* *
53238969 GTATACGTGAACAGTACT
1 GTATACGTGAATAGTACC
*
53238987 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* *
53239005 GTATATGTGAATAGTATC
1 GTATACGTGAATAGTACC
*
53239023 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* *
53239041 ATAAACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* *
53239059 GTATACATGAATAGTGCC
1 GTATACGTGAATAGTACC
*
53239077 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
53239095 GTA
1 GTA
53239098 AACGATCGTA
Statistics
Matches: 91, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 91 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:53239027 original size:36 final size:36
Alignment explanation
Indices: 53238970--53239097 Score: 193
Period size: 36 Copynumber: 3.6 Consensus size: 36
53238960 CCAACTACTG
* * *
53238970 TATACGTGAACAGTACTGTATACGTGAATAGTGCCG
1 TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
* *
53239006 TATATGTGAATAGTATCGTATACGTGAATAGTGCCA
1 TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
* *
53239042 TAAACGTGAATAGTACCGTATACATGAATAGTGCCA
1 TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
53239078 TATACGTGAATAGTACCGTA
1 TATACGTGAATAGTACCGTA
53239098 AACGATCGTA
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (36 bp):
TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
Found at i:53240330 original size:313 final size:311
Alignment explanation
Indices: 53239693--53240568 Score: 1130
Period size: 313 Copynumber: 2.8 Consensus size: 311
53239683 TGATGTTGTT
* * * *
53239693 GATGTTATTTTTGGTATAGTTAGAAGTTTAGTTTTCTATTATAATATAATTAAAG-TTTTACTAA
1 GATGTTATTTTTGGTATAGTTGGAGGTTTAGTTTTCTTTTATAATGTAATT-AAGCTTTTACTAA
* * * *
53239757 TGATTAAGTTAAATTATA-CTTTTTTTATTGTGTTA-ATTTTTAAAGCCACTTTGATATCTAAAG
65 TGATTAAGCTAAATTATACCTTTTCTTATTGTGTTAGTTTTTTTAA-CCACTTTGATATCTAAAG
* * *
53239820 TTACTTTTCATTTAGTCATTTATCGATTTAAGGGAGGTACGAATGTTGCAGACAACATTGTTGGT
129 TTA-TTTTCATTTAGTCATTTATCGATTTAAGGGAGGTATGAATGTTGGAGACGACATTGTTGGT
* * * * *
53239885 -AGTGTAGTCATAAATTTGGATTATGAAAACGAGAAAAAAAGGTATAATTGAAGACGAAATAATG
193 AAG-GCAGTCATAAACTTGGATTATGAAAATGAGAAAAAAA-GTATAATTGAAGGCGAAATGATG
* * * *
53239949 AATGTTATCCATAGACTTGTAACATTTGAATTTCGAACTTATCATGTGATGTTATG
256 AATGTTATCCATAGACTTGTAAAATTTGAATATCGAACTTATCATGTGACGTTAAG
* * * **
53240005 GATGTT-TTTTTGGTATAATTGGAGGTGTAGTTTTCTTTTATAATGTGATTAAGCTTTTTTTAAT
1 GATGTTATTTTTGGTATAGTTGGAGGTTTAGTTTTCTTTTATAATGTAATTAAGCTTTTACTAAT
* *
53240069 AATTAAGCTAAATTATACCGTTTTCTTATTGTGTTAGTTTTTTTAACCACTTTTATATCTAAAGT
66 GATTAAGCTAAATTATACC-TTTTCTTATTGTGTTAGTTTTTTTAACCACTTTGATATCTAAAGT
* **
53240134 TATGTTTCATTTAGTCATTTATCAATTTTGGGGAGGTATGAATGTTGGAGACGACATTGTTGGTA
130 TAT-TTTCATTTAGTCATTTATCGATTTAAGGGAGGTATGAATGTTGGAGACGACATTGTTGGTA
* * * *
53240199 AGGCAGTCATAAACCTGGATTATCAAAATGAGAAAAATAGTATAATTGAAGGTGAAATGATGAAT
194 AGGCAGTCATAAACTTGGATTATGAAAATGAGAAAAAAAGTATAATTGAAGGCGAAATGATGAAT
* *
53240264 GTTATCCATGGACTTGTAAAATTTGAATATGGAACTTATCATGTGACGTTAAG
259 GTTATCCATAGACTTGTAAAATTTGAATATCGAACTTATCATGTGACGTTAAG
*
53240317 GATGTTATTTTTGGTATAGTTGGAGGTTTAGTTTTCTTGTATAATGTAATTAAGCTTTTACTAAT
1 GATGTTATTTTTGGTATAGTTGGAGGTTTAGTTTTCTTTTATAATGTAATTAAGCTTTTACTAAT
* * * * *
53240382 GATTAAGCTAGATTATACTATTTTCTTA-------AGTTTTTTTAACCACTTTGATGTTTAGAGT
66 GATTAAGCTAAATTATAC-CTTTTCTTATTGTGTTAGTTTTTTTAACCACTTTGATATCTAAAGT
* * *
53240440 TATATTTTATTTAGTCATTTATCGATTTAAAGGAGGTATGAATGTTGGAGACGAAATTGTTGAG-
130 TAT-TTTCATTTAGTCATTTATCGATTTAAGGGAGGTATGAATGTTGGAGACGACATTGTTG-GT
* * * *
53240504 AAGGCAGTCATAAACTTGGATTATGGAAATGAGAAAAACATTATAATTGAATGCGAAATGATGAA
193 AAGGCAGTCATAAACTTGGATTATGAAAATGAGAAAAAAAGTATAATTGAAGGCGAAATGATGAA
53240569 CTTGTGAAAT
Statistics
Matches: 492, Mismatches: 63, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
306 139 0.28
307 1 0.00
310 3 0.01
311 60 0.12
312 84 0.17
313 196 0.40
314 9 0.02
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (311 bp):
GATGTTATTTTTGGTATAGTTGGAGGTTTAGTTTTCTTTTATAATGTAATTAAGCTTTTACTAAT
GATTAAGCTAAATTATACCTTTTCTTATTGTGTTAGTTTTTTTAACCACTTTGATATCTAAAGTT
ATTTTCATTTAGTCATTTATCGATTTAAGGGAGGTATGAATGTTGGAGACGACATTGTTGGTAAG
GCAGTCATAAACTTGGATTATGAAAATGAGAAAAAAAGTATAATTGAAGGCGAAATGATGAATGT
TATCCATAGACTTGTAAAATTTGAATATCGAACTTATCATGTGACGTTAAG
Found at i:53250396 original size:9 final size:10
Alignment explanation
Indices: 53250375--53250418 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
53250365 CTCGATTTAA
53250375 TTTTTAAATT
1 TTTTTAAATT
53250385 TTTTTAAATT
1 TTTTTAAATT
*
53250395 TTTTTGAAAATC
1 TTTTT--AAATT
*
53250407 ATTTTAAATT
1 TTTTTAAATT
53250417 TT
1 TT
53250419 CCAAATACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 20 0.71
12 8 0.29
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:53256630 original size:16 final size:16
Alignment explanation
Indices: 53256609--53256641 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
53256599 TCTATGCCTA
53256609 TCAGATATAAATAATT
1 TCAGATATAAATAATT
53256625 TCAGATATAAATAATT
1 TCAGATATAAATAATT
53256641 T
1 T
53256642 AAATTACACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
TCAGATATAAATAATT
Found at i:53257005 original size:99 final size:99
Alignment explanation
Indices: 53256710--53257006 Score: 289
Period size: 99 Copynumber: 3.0 Consensus size: 99
53256700 GAAAGGCTCT
* * * * * * * * * *
53256710 CAGAAGATGGAGTTTATACAGATCAACCAATTTACTCAGAACCTAGGGTTAACTCAGTTCAAGCA
1 CAGAAGACGGAATTTATACGGTTCAACCAGTTTCCTCGGGACATAGGGTTAACTCAGTTCAAACA
* * * *
53256775 AACCAGTTTAATAATCATATTGGAAGTAGCCTAC
66 AATCAGTTCAATAGTCATATTGGAAGTAGCCTTC
* * * * * *
53256809 CAGAAGATGGAGTTTATACGGTTCAATCGGTTTGCTCGGGATATAGGGTTAACTC-GATTCAAGA
1 CAGAAGACGGAATTTATACGGTTCAACCAGTTTCCTCGGGACATAGGGTTAACTCAG-TTCAA-A
* * *
53256873 -AAATAAGTTCAATAGTCATATTAGAAATAGCCTTC
64 CAAATCAGTTCAATAGTCATATTGGAAGTAGCCTTC
*
53256908 CAGAAGACGGAATTTATAC-TTCTCAACCAGTTTCCTC-GGAGCATAGGGTTAACTCAGTTCAAA
1 CAGAAGACGGAATTTATACGGT-TCAACCAGTTTCCTCGGGA-CATAGGGTTAACTCAGTTCAAA
*
53256971 CAAATCA-TCTCAATGGTCATATTGGAAGTAGCCTTC
64 CAAATCAGT-TCAATAGTCATATTGGAAGTAGCCTTC
53257007 AAGCTGAGCT
Statistics
Matches: 162, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
98 7 0.04
99 154 0.95
100 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (99 bp):
CAGAAGACGGAATTTATACGGTTCAACCAGTTTCCTCGGGACATAGGGTTAACTCAGTTCAAACA
AATCAGTTCAATAGTCATATTGGAAGTAGCCTTC
Found at i:53261928 original size:25 final size:25
Alignment explanation
Indices: 53261897--53261946 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
53261887 AATTAAGTTT
53261897 GTGAAAATTATGTCAAGTAATTAAC
1 GTGAAAATTATGTCAAGTAATTAAC
53261922 GTGAAAATTATGTCAAGTAATTAAC
1 GTGAAAATTATGTCAAGTAATTAAC
53261947 CTATTGTAGT
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (25 bp):
GTGAAAATTATGTCAAGTAATTAAC
Found at i:53274171 original size:22 final size:25
Alignment explanation
Indices: 53274115--53274172 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 25
53274105 CATTAAGGAA
*
53274115 TATTTAATTAATATTTTCTAATTTT
1 TATTCAATTAATATTTTCTAATTTT
*
53274140 TTTTGC-ATTAAT-TTTT-T-ATTTT
1 TATT-CAATTAATATTTTCTAATTTT
53274162 TATTCAATTAA
1 TATTCAATTAA
53274173 AAATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 1 0.04
22 13 0.46
23 1 0.04
24 4 0.14
25 9 0.32
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (25 bp):
TATTCAATTAATATTTTCTAATTTT
Found at i:53274747 original size:27 final size:28
Alignment explanation
Indices: 53274703--53274756 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
53274693 AACGTTACAA
*
53274703 ATTAAAAAGAAAATGTTACCAAATAACT
1 ATTAAAAAGAAAACGTTACCAAATAACT
*
53274731 ATTAAAAA-TAAACGTTACCAAATAAC
1 ATTAAAAAGAAAACGTTACCAAATAAC
53274757 GTTACAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.57, C:0.13, G:0.06, T:0.24
Consensus pattern (28 bp):
ATTAAAAAGAAAACGTTACCAAATAACT
Found at i:53276373 original size:11 final size:11
Alignment explanation
Indices: 53276357--53276381 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53276347 ATGCATCAAG
53276357 ATTATTCTTTT
1 ATTATTCTTTT
53276368 ATTATTCTTTT
1 ATTATTCTTTT
53276379 ATT
1 ATT
53276382 TAGTATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTATTCTTTT
Found at i:53279185 original size:12 final size:11
Alignment explanation
Indices: 53279157--53279190 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
53279147 GATAAAAAAG
*
53279157 TTTGCTACTTT
1 TTTGCTATTTT
53279168 TTTGCTATTTT
1 TTTGCTATTTT
53279179 ATTTGCTATTTT
1 -TTTGCTATTTT
53279191 CTCCCTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.68
Consensus pattern (11 bp):
TTTGCTATTTT
Found at i:53283251 original size:27 final size:26
Alignment explanation
Indices: 53283215--53283265 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
53283205 AATCTGAGTC
53283215 AAAAAATTATTAAATATTATTATCCA
1 AAAAAATTATTAAATATTATTATCCA
53283241 AAAAAATTTATTAAATATTATTATC
1 AAAAAA-TTATTAAATATTATTATC
53283266 TGTGTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (26 bp):
AAAAAATTATTAAATATTATTATCCA
Found at i:53286624 original size:18 final size:18
Alignment explanation
Indices: 53286593--53286627 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53286583 ATTTTAAATA
53286593 AATTATTTCTTTATTTTG
1 AATTATTTCTTTATTTTG
53286611 AATT-TTTCTGTTATTTT
1 AATTATTTCT-TTATTTT
53286628 AATATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.69
Consensus pattern (18 bp):
AATTATTTCTTTATTTTG
Found at i:53286642 original size:15 final size:16
Alignment explanation
Indices: 53286622--53286654 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53286612 ATTTTTCTGT
*
53286622 TATTTT-AATATTAAA
1 TATTTTAAAAATTAAA
53286637 TATTTTAAAAATTAAA
1 TATTTTAAAAATTAAA
53286653 TA
1 TA
53286655 GCATTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTTAAAAATTAAA
Found at i:53286703 original size:12 final size:12
Alignment explanation
Indices: 53286686--53286715 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
53286676 AATTAGTTAA
53286686 ATATTTTTAATT
1 ATATTTTTAATT
53286698 ATATTTTTAATT
1 ATATTTTTAATT
53286710 ATATTT
1 ATATTT
53286716 CCTTTTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTTTTAATT
Found at i:53287047 original size:26 final size:26
Alignment explanation
Indices: 53287006--53287058 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
53286996 TTTTGGACAT
*
53287006 ATTCATAATCAAATATGTGATTTTGG
1 ATTCATAACCAAATATGTGATTTTGG
*
53287032 ATTCATAACCATATATGTGATTTTGG
1 ATTCATAACCAAATATGTGATTTTGG
53287058 A
1 A
53287059 CAACTTTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (26 bp):
ATTCATAACCAAATATGTGATTTTGG
Found at i:53287574 original size:26 final size:26
Alignment explanation
Indices: 53287533--53287582 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
53287523 TTTTGGACAT
*
53287533 ATTCATAACTAAATATGTGATTTTGG
1 ATTCATAACCAAATATGTGATTTTGG
*
53287559 ATTCATAACCATATATGTGATTTT
1 ATTCATAACCAAATATGTGATTTT
53287583 TGGACAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (26 bp):
ATTCATAACCAAATATGTGATTTTGG
Found at i:53288295 original size:97 final size:95
Alignment explanation
Indices: 53288177--53288470 Score: 252
Period size: 97 Copynumber: 3.0 Consensus size: 95
53288167 GACATTTGTA
* *
53288177 AAACACCTGTAATATTAAGAACCGCATAAGAATAAATGAAGATGATGGTTTGTATTTGAACTCTA
1 AAACACATGTAATATTAAGAACTGCATAAGAATAAATGAAGAT-ATGGTTTGTATTTGAACTCTA
53288242 AAAATCAAATCAATTAAATCATCGATCTTCAC
65 AAAATCAAATCAATTAAAT-ATCGATCTTCAC
* * * * * ** *
53288274 AAACACGTGTAATATTGAGAACTACATATGAATAAATGAAGACAATAATTTATATTTGAATCTCG
1 AAACACATGTAATATTAAGAACTGCATAAGAATAAATGAAGA-TATGGTTTGTATTTGAA-CTC-
* * *
53288339 T--AAATTAAATAAATTATAATATCGATATT-AGC
63 TAAAAATCAAATCAATTA-AATATCGATCTTCA-C
* * * * * * **
53288371 AAAACACATGTAATATTAAGAATTGCTTAAGAACAAATGAGGACTATGGTATGTATTTTAACAAT
1 -AAACACATGTAATATTAAGAACTGCATAAGAATAAATGAAGA-TATGGTTTGTATTTGAACTCT
* ** *
53288436 AAAAATCAATTCAATTATAGGATCAATCTTCAC
64 AAAAATCAAATCAATTA-AATATCGATCTTCAC
53288469 AA
1 AA
53288471 GTATGTGTAA
Statistics
Matches: 153, Mismatches: 35, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
96 2 0.01
97 75 0.49
98 74 0.48
99 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (95 bp):
AAACACATGTAATATTAAGAACTGCATAAGAATAAATGAAGATATGGTTTGTATTTGAACTCTAA
AAATCAAATCAATTAAATATCGATCTTCAC
Found at i:53288428 original size:98 final size:95
Alignment explanation
Indices: 53288144--53288428 Score: 261
Period size: 97 Copynumber: 2.9 Consensus size: 95
53288134 TTTAATCCTA
* * * * * * *
53288144 TAAATTAAACAAATTATAAGATTGACATTTGTAAAACACCTGTAATATTAAGAACCGCATAAGAA
1 TAAATTAAATAAATTATAATATCGATA-TTGCAAAACACATGTAATATTAAGAACTGCATAAGAA
53288209 TAAATGAAGA-TGATGGTTTGTATTTGAACTC
65 TAAATGAAGACT-ATGGTTTGTATTTGAACTC
* * * * * * *
53288240 TAAAAATCAAATCAATTA-AATCATCGATCTT-CACAAACACGTGTAATATTGAGAACTACATAT
1 T--AAATTAAATAAATTATAAT-ATCGATATTGCA-AAACACATGTAATATTAAGAACTGCATAA
* ** *
53288303 GAATAAATGAAGACAATAATTTATATTTGAATCTC
62 GAATAAATGAAGACTATGGTTTGTATTTGAA-CTC
* *
53288338 GTAAATTAAATAAATTATAATATCGATATTAGCAAAACACATGTAATATTAAGAATTGCTTAAGA
1 -TAAATTAAATAAATTATAATATCGATATT-GCAAAACACATGTAATATTAAGAACTGCATAAGA
* * *
53288403 ACAAATGAGGACTATGGTATGTATTT
64 ATAAATGAAGACTATGGTTTGTATTT
53288429 TAACAATAAA
Statistics
Matches: 146, Mismatches: 33, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
96 2 0.01
97 75 0.51
98 66 0.45
99 3 0.02
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (95 bp):
TAAATTAAATAAATTATAATATCGATATTGCAAAACACATGTAATATTAAGAACTGCATAAGAAT
AAATGAAGACTATGGTTTGTATTTGAACTC
Found at i:53288428 original size:195 final size:195
Alignment explanation
Indices: 53288122--53288597 Score: 508
Period size: 195 Copynumber: 2.4 Consensus size: 195
53288112 GAATGACCAT
* * * * * * * *
53288122 AATAATTTCTATTTTAATCCTATAAATTAAACAAATTATAAGATTGACATTTGTAAAACACCTGT
1 AATAATTTATATTTGAATCCAATAAATTAAATAAATTATAAGATCGACATTAGCAAAACACATGT
* * **
53288187 AATATTAAGAACCGCATAAGAATAAATGAAGATGATGGTTTGTATTTGAACTCTAAAAATCAAAT
66 AATATTAAGAACCGCATAAGAACAAATGAAGATGATGGTATGTATTTGAACAATAAAAATCAAAT
* * * *
53288252 CAATTAAATCATCGATCTTCACAAACACGTGTAATATTGAGAACTACATATGAATAAATGAAGAC
131 CAATTAAAGCATCAATCTTCACAAACACGTGTAACATTAAGAACTACATATGAATAAATGAAGAC
* * *
53288317 AATAATTTATATTTGAATCTC-GTAAATTAAATAAATTATAATATCGATATTAGCAAAACACATG
1 AATAATTTATATTTGAATC-CAATAAATTAAATAAATTATAAGATCGACATTAGCAAAACACATG
** * * *
53288381 TAATATTAAGAATTGCTTAAGAACAAATGAGGACT-ATGGTATGTATTTTAACAATAAAAATCAA
65 TAATATTAAGAACCGCATAAGAACAAATGAAGA-TGATGGTATGTATTTGAACAATAAAAATCAA
* * * ** * * * * * *
53288445 TTCAATTATAGGATCAATCTTCACAAGTATGTGTAACATTAAGAATTGCGTATGAATGAATGAAT
129 ATCAATTAAAGCATCAATCTTCACAAACACGTGTAACATTAAGAACTACATATGAATAAATGAAG
53288510 AC
194 AC
* * *** * *
53288512 AATAATTTATCTTTGAAGCCAATAAATTAAATAAATTATAAGATTTTTC-TTTGCAAAACACGTG
1 AATAATTTATATTTGAATCCAATAAATTAAATAAATTATAAGA-TCGACATTAGCAAAACACATG
* *
53288576 CAATATTAAGAACAGCATAAGA
65 TAATATTAAGAACCGCATAAGA
53288598 TTTAATGAAG
Statistics
Matches: 229, Mismatches: 48, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
194 1 0.00
195 225 0.98
196 3 0.01
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (195 bp):
AATAATTTATATTTGAATCCAATAAATTAAATAAATTATAAGATCGACATTAGCAAAACACATGT
AATATTAAGAACCGCATAAGAACAAATGAAGATGATGGTATGTATTTGAACAATAAAAATCAAAT
CAATTAAAGCATCAATCTTCACAAACACGTGTAACATTAAGAACTACATATGAATAAATGAAGAC
Found at i:53291670 original size:85 final size:86
Alignment explanation
Indices: 53291525--53291685 Score: 218
Period size: 86 Copynumber: 1.9 Consensus size: 86
53291515 TTTTTTGTAT
* * * *
53291525 TCAATTGAGCACTTGAACTTTTCAAATGCATCAAAAAGGCCCTCAAACTTCTTCAAAAAAAGCAA
1 TCAATTGAGCACTTGAACTTTTCAAATGCATAAAAAAGACCCTCAAAATTCTTCAAAAAAAGAAA
53291590 TAAAGCCCCTGTTTTTTTCAC
66 TAAAGCCCCTGTTTTTTTCAC
* * **
53291611 TCAATTGAGTACTTGAAC-TTTCAAAATGTATAAAAAAGACCCTCAAAATT-TTTTAAAAAAGAA
1 TCAATTGAGCACTTGAACTTTTC-AAATGCATAAAAAAGACCCTCAAAATTCTTCAAAAAAAGAA
*
53291674 ATTAAGCCCCTG
65 ATAAAGCCCCTG
53291686 CTCTTATTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
85 25 0.38
86 40 0.62
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (86 bp):
TCAATTGAGCACTTGAACTTTTCAAATGCATAAAAAAGACCCTCAAAATTCTTCAAAAAAAGAAA
TAAAGCCCCTGTTTTTTTCAC
Found at i:53291727 original size:20 final size:21
Alignment explanation
Indices: 53291704--53291748 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
53291694 TATAAAAAAT
53291704 AAAAAATATTAAATTTT-ATA
1 AAAAAATATTAAATTTTAATA
53291724 AAAAAATATTAAATTTTAATA
1 AAAAAATATTAAATTTTAATA
53291745 AAAA
1 AAAA
53291749 TATAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAAATATTAAATTTTAATA
Found at i:53291737 original size:27 final size:26
Alignment explanation
Indices: 53291692--53291758 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 26
53291682 CCTGCTCTTA
53291692 TTTATAAAAAATAAAAAATATTAAAT
1 TTTATAAAAAATAAAAAATATTAAAT
53291718 TTTAT-----A-AAAAAATATTAAAT
1 TTTATAAAAAATAAAAAATATTAAAT
53291738 TTTAATAAAAATATAAAAAAT
1 TTT-ATAAAAA-ATAAAAAAT
53291759 TAAAAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
20 17 0.52
21 3 0.09
26 5 0.15
27 1 0.03
28 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
TTTATAAAAAATAAAAAATATTAAAT
Found at i:53291770 original size:10 final size:10
Alignment explanation
Indices: 53291703--53291777 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
53291693 TTATAAAAAA
*
53291703 TAAAAAATAT
1 TAAAAATTAT
**
53291713 TAAATTTTAT
1 TAAAAATTAT
* *
53291723 AAAAAAATAT
1 TAAAAATTAT
** *
53291733 TAAATTTTAA
1 TAAAAATTAT
53291743 TAAAAA-TA-
1 TAAAAATTAT
53291751 TAAAAA--AT
1 TAAAAATTAT
53291759 TAAAAATTAT
1 TAAAAATTAT
53291769 TAAAAATTA
1 TAAAAATTA
53291778 GATTTTTTTT
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
7 1 0.02
8 12 0.25
9 2 0.04
10 33 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:53291772 original size:26 final size:27
Alignment explanation
Indices: 53291725--53291775 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
53291715 AATTTTATAA
**
53291725 AAAAATATTAAATTTTAATAAAAATAT
1 AAAAATATTAAAAATTAATAAAAATAT
*
53291752 AAAAA-ATTAAAAATTATTAAAAAT
1 AAAAATATTAAAAATTAATAAAAAT
53291776 TAGATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAAATATTAAAAATTAATAAAAATAT
Found at i:53291773 original size:17 final size:16
Alignment explanation
Indices: 53291743--53291777 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
53291733 TAAATTTTAA
53291743 TAAAAATATAAAAAAT
1 TAAAAATATAAAAAAT
*
53291759 TAAAAATTATTAAAAAT
1 TAAAAA-TATAAAAAAT
53291776 TA
1 TA
53291778 GATTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAAATATAAAAAAT
Found at i:53292072 original size:28 final size:28
Alignment explanation
Indices: 53291986--53292076 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 28
53291976 TTTTACGAAA
* *
53291986 TTTATATTTCTTTACATTTTGTATAATTTT
1 TTTATATTTCTATA-AATTT-TATAATTTT
* *
53292016 CTTATGACTT-TATAAAATTTTATAATTTT
1 TTTAT-ATTTCTAT-AAATTTTATAATTTT
*
53292045 TTTATATTTCTATATATTTTATAATTTT
1 TTTATATTTCTATAAATTTTATAATTTT
53292073 TTTA
1 TTTA
53292077 CGATTTTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 21 0.41
29 16 0.31
30 10 0.20
31 4 0.08
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTATATTTCTATAAATTTTATAATTTT
Found at i:53297041 original size:16 final size:16
Alignment explanation
Indices: 53297020--53297101 Score: 65
Period size: 17 Copynumber: 4.6 Consensus size: 16
53297010 CCCATTATGC
53297020 TTATTTTATTTATTTA
1 TTATTTTATTTATTTA
53297036 TTATTTGTTATATTATTTA
1 TTA-TT-TTAT-TTATTTA
* * *
53297055 TTTTTATTTTACTAATTTT
1 ---TTATTTTATTTATTTA
53297074 TTATTTTATTTTATTTA
1 TTATTTTA-TTTATTTA
53297091 TTATTCTTATT
1 TTATT-TTATT
53297102 CTCAGATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
16 11 0.21
17 14 0.27
18 7 0.13
19 12 0.23
20 3 0.06
21 2 0.04
22 3 0.06
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.73
Consensus pattern (16 bp):
TTATTTTATTTATTTA
Found at i:53297051 original size:23 final size:22
Alignment explanation
Indices: 53297020--53297063 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
53297010 CCCATTATGC
*
53297020 TTATTTTATTTATTTATTATTTG
1 TTATATTATTTATTT-TTATTTG
53297043 TTATATTATTTATTTTTATTT
1 TTATATTATTTATTTTTATTT
53297064 TACTAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (22 bp):
TTATATTATTTATTTTTATTTG
Found at i:53303233 original size:15 final size:15
Alignment explanation
Indices: 53303196--53303237 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
53303186 TTATAAAAAT
* *
53303196 ATAATAACAACAGTA
1 ATAATAATAATAGTA
53303211 ATAATAATAATAGTA
1 ATAATAATAATAGTA
*
53303226 ATATTAATAATA
1 ATAATAATAATA
53303238 ATAGTAGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (15 bp):
ATAATAATAATAGTA
Found at i:53303505 original size:24 final size:24
Alignment explanation
Indices: 53303478--53303550 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
53303468 TTGAAGGAAT
53303478 AATAATAAATAAATAATAAATGAA
1 AATAATAAATAAATAATAAATGAA
**
53303502 AATAAGT--ATAGGTAAATAAAT-AA
1 AATAA-TAAATAAAT-AATAAATGAA
* * *
53303525 AATAATAAGTAAATAAAAAAGGAA
1 AATAATAAATAAATAATAAATGAA
53303549 AA
1 AA
53303551 AAATGCCTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
22 1 0.03
23 16 0.43
24 19 0.51
25 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (24 bp):
AATAATAAATAAATAATAAATGAA
Found at i:53303536 original size:20 final size:24
Alignment explanation
Indices: 53303492--53303541 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 24
53303482 ATAAATAAAT
53303492 AATAAATGAAAATAAGTATAGGTA
1 AATAAATGAAAATAAGTATAGGTA
53303516 AATAAAT-AAAATAA-TA-A-GTA
1 AATAAATGAAAATAAGTATAGGTA
53303536 AATAAA
1 AATAAA
53303542 AAAGGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.35
21 1 0.04
22 2 0.08
23 7 0.27
24 7 0.27
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (24 bp):
AATAAATGAAAATAAGTATAGGTA
Found at i:53309126 original size:16 final size:16
Alignment explanation
Indices: 53309105--53309135 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53309095 AATACTTCTC
53309105 AAAAATACTTTTGGGA
1 AAAAATACTTTTGGGA
53309121 AAAAATACTTTTGGG
1 AAAAATACTTTTGGG
53309136 CTACTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (16 bp):
AAAAATACTTTTGGGA
Found at i:53309719 original size:35 final size:34
Alignment explanation
Indices: 53309673--53309741 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 34
53309663 TCTTAGAAAG
53309673 AAAGATTGAAGAGCAAATTCTTTGAACTCTTTCC
1 AAAGATTGAAGAGCAAATTCTTTGAACTCTTTCC
53309707 NAAAGATTGAAGAGCAAATTCTTTGAACTCTTTCC
1 -AAAGATTGAAGAGCAAATTCTTTGAACTCTTTCC
53309742 CTTCGACCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.32
Consensus pattern (34 bp):
AAAGATTGAAGAGCAAATTCTTTGAACTCTTTCC
Found at i:53311261 original size:21 final size:21
Alignment explanation
Indices: 53311235--53311277 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
53311225 ATGGTTCTAA
*
53311235 AGATCACAAACGCGTTGTAAT
1 AGATCACAAACGCGTTGCAAT
53311256 AGATCACAAACGCGTTGCAAT
1 AGATCACAAACGCGTTGCAAT
53311277 A
1 A
53311278 AGCTTACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AGATCACAAACGCGTTGCAAT
Found at i:53311409 original size:2 final size:2
Alignment explanation
Indices: 53311397--53311426 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53311387 CTATTCTCTA
*
53311397 GT GT CT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
53311427 TTTAATCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.47, T:0.50
Consensus pattern (2 bp):
GT
Found at i:53316332 original size:18 final size:19
Alignment explanation
Indices: 53316309--53316346 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
53316299 GGAAGCAAGC
*
53316309 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
53316327 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
53316346 A
1 A
53316347 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:53323124 original size:7 final size:7
Alignment explanation
Indices: 53323114--53323138 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53323104 TTATAATTTG
53323114 ATTGATA
1 ATTGATA
53323121 ATTGATA
1 ATTGATA
53323128 ATTGATA
1 ATTGATA
53323135 ATTG
1 ATTG
53323139 GTATGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (7 bp):
ATTGATA
Found at i:53323981 original size:56 final size:56
Alignment explanation
Indices: 53323914--53324028 Score: 221
Period size: 56 Copynumber: 2.1 Consensus size: 56
53323904 ACCTAAACAA
*
53323914 TTACCTTAATTACATGATACACTAGTGTATATATATGATACATATGATATGGTCAC
1 TTACCTTAATTACATGATACACTAGTATATATATATGATACATATGATATGGTCAC
53323970 TTACCTTAATTACATGATACACTAGTATATATATATGATACATATGATATGGTCAC
1 TTACCTTAATTACATGATACACTAGTATATATATATGATACATATGATATGGTCAC
53324026 TTA
1 TTA
53324029 ATTTGGCTTC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (56 bp):
TTACCTTAATTACATGATACACTAGTATATATATATGATACATATGATATGGTCAC
Found at i:53330266 original size:27 final size:28
Alignment explanation
Indices: 53330236--53330289 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
53330226 TTTGTCATTG
53330236 TTGTTATTTTCT-GTTTACTTA-GTTTCT
1 TTGTTATTTTCTCGTTT-CTTAGGTTTCT
*
53330263 TTGTTGTTTTCTCGTTTCTTAGGTTTC
1 TTGTTATTTTCTCGTTTCTTAGGTTTC
53330290 AAGACAGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.07, C:0.13, G:0.15, T:0.65
Consensus pattern (28 bp):
TTGTTATTTTCTCGTTTCTTAGGTTTCT
Found at i:53333667 original size:106 final size:108
Alignment explanation
Indices: 53333488--53333782 Score: 346
Period size: 108 Copynumber: 2.8 Consensus size: 108
53333478 TATTTAGTCG
* *
53333488 AACGAGAAATCGAAACCCAGCACATTAGGGCATGTTCTCTCGAATTTCCAAACGCAAAACATTGC
1 AACGAGAAATCGAAACCCAGCACATTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAATATTGC
** **
53333553 CTCGTTTTAGAA-TTTCGAAAGGATATTCGACTA-TTTGGCCA
66 CTTATTTTAGAATTTTAAAAAGGATATTCGACTATTTTGGCCA
* * * * * * *
53333594 AACGAGTAATCGAAACCCAACATATTAGGGCACGTTTTCTCGAATTTCCAAACGCGAAATATGGT
1 AACGAGAAATCGAAACCCAGCACATTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAATATTGC
* * * * * *
53333659 CTTATTTTAAAATTTTAAAAAGGGTATTTGGCTATTTTGGTCG
66 CTTATTTTAGAATTTTAAAAAGGATATTCGACTATTTTGGCCA
* * *
53333702 AACGAGAAATCAAAACCCAGCACGTTAGGGCATGTTTTCTC-AATTTTTCAAACGCAAAATATTG
1 AACGAGAAATCGAAACCCAGCACATTAGGGCATGTTTTCTCGAA-TTTCCAAACGCAAAATATTG
53333766 CCTTA-TTTAGAAATTTT
65 CCTTATTTTAG-AATTTT
53333783 TCTTTTTTAT
Statistics
Matches: 155, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
106 65 0.42
107 22 0.14
108 68 0.44
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (108 bp):
AACGAGAAATCGAAACCCAGCACATTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAATATTGC
CTTATTTTAGAATTTTAAAAAGGATATTCGACTATTTTGGCCA
Found at i:53333731 original size:108 final size:105
Alignment explanation
Indices: 53333454--53333781 Score: 372
Period size: 106 Copynumber: 3.1 Consensus size: 105
53333444 ACGACATGGA
* * *
53333454 TTAAAATTTAAGAGGATATTGGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACATTAGGGC
1 TTAAAATTTAAAAGGATATTCGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGC
* * **
53333519 ATGTTCTCTCGAATTTCCAAACGCAAAACATTGCCTCGTT
66 ATGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTATT
* * * * * * * *
53333559 TTAGAATTTCGAAAGGATATTCGACTATTTGGCCAAACGAGTAATCGAAACCCAACATATTAGGG
1 TTAAAATTT-AAAAGGATATTCGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGG
* * * *
53333624 CACGTTTTCTCGAATTTCCAAACGCGAAATATGGTCTTATT
65 CATGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTATT
* * * *
53333665 TTAAAATTTTAAAAAGGGTATTTGGCTATTTTGGTCGAACGAGAAATCAAAACCCAGCACGTTAG
1 TTAAAA-TTT-AAAAGGATATTCGGCTA-TTTGGTCGAACGAGAAATCGAAACCCAGCACATTAG
*
53333730 GGCATGTTTTCTC-AATTTTTCAAACGCAAAATATTGCCTTA-T
63 GGCATGTTTTCTCGAA-TTTCCAAACGCAAAATATTGCCTTATT
53333772 TTAGAAATTT
1 TTA-AAATTT
53333782 TTCTTTTTTA
Statistics
Matches: 181, Mismatches: 37, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
105 8 0.04
106 83 0.46
107 25 0.14
108 65 0.36
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (105 bp):
TTAAAATTTAAAAGGATATTCGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGC
ATGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTATT
Found at i:53334346 original size:18 final size:21
Alignment explanation
Indices: 53334307--53334350 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
53334297 ACATGTATAA
53334307 GTATGTGTATTAATTAAAAAT
1 GTATGTGTATTAATTAAAAAT
53334328 GTATGTGTATT-A-T-AAAAT
1 GTATGTGTATTAATTAAAAAT
53334346 GTATG
1 GTATG
53334351 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
19 1 0.04
20 1 0.04
21 11 0.48
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (21 bp):
GTATGTGTATTAATTAAAAAT
Found at i:53335628 original size:19 final size:19
Alignment explanation
Indices: 53335594--53335634 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
53335584 CTAGGTTTAG
53335594 TTGTATTTGGGTTTGGGTT
1 TTGTATTTGGGTTTGGGTT
53335613 TTGT-TTTGGGTATTGGGTT
1 TTGTATTTGGGT-TTGGGTT
53335632 TTG
1 TTG
53335635 CCTGGGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.05, C:0.00, G:0.37, T:0.59
Consensus pattern (19 bp):
TTGTATTTGGGTTTGGGTT
Found at i:53336162 original size:127 final size:127
Alignment explanation
Indices: 53335991--53336746 Score: 1188
Period size: 127 Copynumber: 6.0 Consensus size: 127
53335981 CTTGATGCGA
*
53335991 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATTCGATCTGCTCCACTACTGCTTAGGGAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGA
* *
53336056 TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCTG
66 TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCCG
* * *
53336118 TCTGCTCCACTACTGGTTAAGGAGATAAGACTTGATGCGATCTGCTGCACTACTGCTTAGGGAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGA
* * * * * * *
53336183 TAAGATCTATGGTTTTAATTCACTTCACTGGAACTTCAAGGAGATAGGATTGGTTTCTTCCA
66 TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCCG
* *
53336245 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGATCTACTCCACTACTGCTTAGGGAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGA
* * *
53336310 TAAGATCTATGGTTTTAATCCGCTCCACTACAACTTTAGGGAGATAGGATTGGTTTCTTCCG
66 TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCCG
* * *
53336372 TCTGCTTCACTACTACTTAGGGAGATAAGACTTGATACGATCTGCTCCACTACTGCTTAGGGAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGA
* * *
53336437 TAAGATCTGTGGTTTTAATCCACTCCACTGCAACTTCAAGGAGATAGGATTGGTTTCTTCCA
66 TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCCG
* * * *
53336499 TCTACTCTACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTACTTAGAGAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGA
* * * *
53336564 TAAGATTTGTGGTTTTAATCAGCTCCACTACAACTTTAGGGAGATAGGATTGGTTTCTTCCG
66 TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCCG
* * *
53336626 TCTGCTCCACTACTGCTTAAGGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAAGGAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGA
*
53336691 TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTGGTTT
66 TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTT
53336747 TTTTCTTTTT
Statistics
Matches: 566, Mismatches: 63, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
127 566 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (127 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGA
TAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCCG
Found at i:53336827 original size:50 final size:50
Alignment explanation
Indices: 53336773--53337224 Score: 173
Period size: 50 Copynumber: 9.1 Consensus size: 50
53336763 TGTCTATGCT
* *
53336773 AGGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTC
1 AGGGAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTTAACTGCAATGTC
* * * * * * * * ** * *
53336823 AGGGAAGCAAGATTTGCCATCGTAGCTTTAATATGTTCCACTGCACTGCC
1 AGGGAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTTAACTGCAATGTC
* * * * *
53336873 AGGGAAGTAAGATTTGCTGTTGCGGCCTCAATCTTTTTAATTGCAATGTC
1 AGGGAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTTAACTGCAATGTC
** **** * * ** *
53336923 AGGGAAACAAGATTTTTTGTTTGTAGCTTTAAT-TTGTTCCACTGCACCA-CT-
1 AGGGAAGTAAGATTCGCCG-TTGCAGCTTCAATCTT-TTTAACTGCA--ATGTC
* * * * **
53336974 AGGGGAGTAAGATTCGCCGTTACGGCTTCAATC-TTTTAATTATAATGTC
1 AGGGAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTTAACTGCAATGTC
*** * * * ** ** ** *
53337023 AGGGAAACGAGATTCTCCGTCGTAGCTTCAATCCATTCCACTGCACCGCC
1 AGGGAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTTAACTGCAATGTC
* *
53337073 AAGGG-AGTAAGATTCGCCGTTGCAGCTTCAATC-TTTTAATTGCAATATC
1 -AGGGAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTTAACTGCAATGTC
** * * * * * ** * *
53337122 -GAGGAAACAGGATTCACCGCTGTAGCTTCAATCTGTTCCACTGCACTGCC
1 AG-GGAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTTAACTGCAATGTC
* * * * * * *
53337172 AGGGGAGTAAGATTCACCGTTACGGCTTCAAAC-TTTTAAATGCAATCTC
1 AGGGAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTTAACTGCAATGTC
53337221 AGGG
1 AGGG
53337225 GTACGAGTAA
Statistics
Matches: 270, Mismatches: 119, Indels: 27
0.65 0.29 0.06
Matches are distributed among these distances:
47 2 0.01
48 3 0.01
49 72 0.27
50 158 0.59
51 33 0.12
52 1 0.00
53 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (50 bp):
AGGGAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTTAACTGCAATGTC
Found at i:53337082 original size:99 final size:99
Alignment explanation
Indices: 53336773--53337224 Score: 498
Period size: 99 Copynumber: 4.5 Consensus size: 99
53336763 TGTCTATGCT
*
53336773 AGGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATT-
1 AGGG-AGTAAGATTCGCCGTTGCGGCTTCAATC-TTTTAATTGCAATGTCAGGGAAACAAGATTC
* * * *
53336837 TGCCATCGTAGCTTTAATATGTTCCACTGCACTGCC-
64 T-CCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * *
53336873 AGGGAAGTAAGATTTGCTGTTGCGGCCTCAATCTTTTTAATTGCAATGTCAGGGAAACAAGATTT
1 AGGG-AGTAAGATTCGCCGTTGCGGCTTCAATC-TTTTAATTGCAATGTCAGGGAAACAAGATTC
** * * * * *
53336938 TTTGTTTGTAGCTTTAATTTGTTCCACTGCACCACTA
64 TCCG-TCGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * ** *
53336975 GGGGAGTAAGATTCGCCGTTACGGCTTCAATCTTTTAATTATAATGTCAGGGAAACGAGATTCTC
1 AGGGAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAATTGCAATGTCAGGGAAACAAGATTCTC
**
53337040 CGTCGTAGCTTCAATCCATTCCACTGCACCGCCA
66 CGTCGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * *
53337074 AGGGAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTAATTGCAATATC-GAGGAAACAGGATTCA
1 AGGGAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAATTGCAATGTCAG-GGAAACAAGATTCT
*
53337138 CCG-CTGTAGCTTCAATCTGTTCCACTGCACTGCCA
65 CCGTC-GTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * * * *
53337173 GGGGAGTAAGATTCACCGTTACGGCTTCAAACTTTTAAATGCAATCTCAGGG
1 AGGGAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAATTGCAATGTCAGGG
53337225 GTACGAGTAA
Statistics
Matches: 297, Mismatches: 49, Indels: 13
0.83 0.14 0.04
Matches are distributed among these distances:
98 2 0.01
99 151 0.51
100 90 0.30
101 51 0.17
102 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (99 bp):
AGGGAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAATTGCAATGTCAGGGAAACAAGATTCTC
CGTCGTAGCTTCAATCTGTTCCACTGCACCGCCA
Found at i:53338205 original size:1 final size:1
Alignment explanation
Indices: 53338195--53338238 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
53338185 TGGCCTCTCC
* * * *
53338195 TTTTTCTTTTTTTTTTCTTTTTTTTTTCTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53338239 CCAAGTGAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:53338215 original size:10 final size:11
Alignment explanation
Indices: 53338195--53338238 Score: 81
Period size: 11 Copynumber: 4.1 Consensus size: 11
53338185 TGGCCTCTCC
53338195 TTTTTCTTTTT
1 TTTTTCTTTTT
53338206 TTTTTCTTTTT
1 TTTTTCTTTTT
53338217 TTTTTC-TTTT
1 TTTTTCTTTTT
53338227 TTTTTCTTTTT
1 TTTTTCTTTTT
53338238 T
1 T
53338239 CCAAGTGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.31
11 22 0.69
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:53338220 original size:21 final size:21
Alignment explanation
Indices: 53338195--53338238 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 21
53338185 TGGCCTCTCC
53338195 TTTTTCTTTTTTTTTTCTTTTT
1 TTTTTC-TTTTTTTTTCTTTTT
53338217 TTTTTCTTTTTTTTTCTTTTT
1 TTTTTCTTTTTTTTTCTTTTT
53338238 T
1 T
53338239 CCAAGTGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (21 bp):
TTTTTCTTTTTTTTTCTTTTT
Found at i:53358924 original size:100 final size:100
Alignment explanation
Indices: 53358812--53359020 Score: 346
Period size: 100 Copynumber: 2.1 Consensus size: 100
53358802 ATAAAGAAAA
* *
53358812 ATATATAGATAGAAATTATAAAATATGTATGGAAAGTATAATATATATACGTACATATATATATA
1 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATACGTACATATATATATA
* * * *
53358877 AGTTAATAAATATATAGATCATAAAGATAATGATT
66 AGGTAATAAATATATAAATCATAAAAATAATAATT
*
53358912 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATTATATATATACGTACATATATATATA
1 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATACGTACATATATATATA
53358977 AGGTAATAAATATATAAATCATAAAAATAATAATT
66 AGGTAATAAATATATAAATCATAAAAATAATAATT
*
53359012 ACATATATA
1 ATATATATA
53359021 AACTTAAAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (100 bp):
ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATACGTACATATATATATA
AGGTAATAAATATATAAATCATAAAAATAATAATT
Found at i:53358957 original size:20 final size:20
Alignment explanation
Indices: 53358909--53358960 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
53358899 AAAGATAATG
*
53358909 ATTATATATATATAGAAATT
1 ATTATATATATATAGAAAGT
* * *
53358929 ATAAAATATGTATAGAAAGT
1 ATTATATATATATAGAAAGT
53358949 ATTATATATATA
1 ATTATATATATA
53358961 CGTACATATA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (20 bp):
ATTATATATATATAGAAAGT
Found at i:53359665 original size:17 final size:17
Alignment explanation
Indices: 53359643--53359675 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53359633 TGCCAAGGAG
*
53359643 AAAATAATAATAATAAT
1 AAAATAAAAATAATAAT
53359660 AAAATAAAAATAATAA
1 AAAATAAAAATAATAA
53359676 AAGAACACAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAAAAATAATAAT
Found at i:53359671 original size:14 final size:14
Alignment explanation
Indices: 53359648--53359677 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53359638 AGGAGAAAAT
*
53359648 AATAATAATAATAA
1 AATAAAAATAATAA
53359662 AATAAAAATAATAA
1 AATAAAAATAATAA
53359676 AA
1 AA
53359678 GAACACAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAAAATAATAA
Found at i:53359763 original size:15 final size:16
Alignment explanation
Indices: 53359740--53359772 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53359730 TTTTTTTAAC
53359740 TCTTAATCG-TTTTTT
1 TCTTAATCGATTTTTT
*
53359755 TCTTTATCGATTTTTT
1 TCTTAATCGATTTTTT
53359771 TC
1 TC
53359773 AAAATCCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.12, C:0.15, G:0.06, T:0.67
Consensus pattern (16 bp):
TCTTAATCGATTTTTT
Found at i:53359879 original size:20 final size:19
Alignment explanation
Indices: 53359854--53359919 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
53359844 CTTGTTTACA
53359854 TTGATTTGATTCTCAATCTT
1 TTGATTTGATTCTCAATC-T
** * *
53359874 TTGATTTCTTTC-CATTACA
1 TTGATTTGATTCTCAAT-CT
53359893 TTGATTTGATTCTCAATCCT
1 TTGATTTGATTCTCAAT-CT
53359913 TTGATTT
1 TTGATTT
53359920 CTTTCCATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTGATTTGATTCTCAATCT
Found at i:53359898 original size:19 final size:19
Alignment explanation
Indices: 53359874--53359930 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
53359864 TCTCAATCTT
53359874 TTGATTTCTTTCCATTACA
1 TTGATTTCTTTCCATTACA
** * * *
53359893 TTGATTTGATTCTCAATCCT
1 TTGATTTCTTTC-CATTACA
53359913 TTGATTTCTTTCCATTAC
1 TTGATTTCTTTCCATTAC
53359931 TGTTTTGCTT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.53
Consensus pattern (19 bp):
TTGATTTCTTTCCATTACA
Found at i:53359903 original size:39 final size:39
Alignment explanation
Indices: 53359849--53359930 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
53359839 AAAATCTTGT
*
53359849 TTACATTGATTTGATTCTCAATCTTTTGATTTCTTTCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
53359888 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
53359927 TTAC
1 TTAC
53359931 TGTTTTGCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (39 bp):
TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
Found at i:53360584 original size:44 final size:44
Alignment explanation
Indices: 53360514--53360658 Score: 229
Period size: 44 Copynumber: 3.3 Consensus size: 44
53360504 GTTTACTTTA
* * *
53360514 AACCTATTCCACTGCTAACCAGGGAGATAGGATTCTCAATCTTC
1 AACCTATTCCACTGCTGACCAAGGAGATAGGATTCACAATCTTC
*
53360558 AACCTATTCCACCGCTGACCAAGGAGATAGGATTCACAATCTTC
1 AACCTATTCCACTGCTGACCAAGGAGATAGGATTCACAATCTTC
53360602 AACCTATTCCACTGCTGA-CAAGGGAGATAGGATTCACAATCTTC
1 AACCTATTCCACTGCTGACCAA-GGAGATAGGATTCACAATCTTC
*
53360646 AATCTATTCCACT
1 AACCTATTCCACT
53360659 CCTGCCCAGG
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
43 3 0.03
44 91 0.97
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (44 bp):
AACCTATTCCACTGCTGACCAAGGAGATAGGATTCACAATCTTC
Found at i:53361305 original size:132 final size:132
Alignment explanation
Indices: 53360622--53361297 Score: 1005
Period size: 132 Copynumber: 5.1 Consensus size: 132
53360612 ACTGCTGACA
* * ** *
53360622 AGGGAGATAGGAT-TCACAATCTTCAATCTATTCCACTCCTGCCCAGGGAAGTAGAATTACTGGC
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGC
* * *
53360686 TTCAATGTACTCCGCTGTAACCACAGAGAGGTAAAATCCGCTATATTCGATCTGCTCCGCTACTG
65 TTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCCGCTACTG
53360751 CTT
130 CTT
53360754 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* * * * * *
53360819 TCAATGTACTCCACTATAACCACAAAAAGGTAAAATCTGTCATCTTCGATCTGCTTCGCTACTGC
66 TCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCCGCTACTGC
53360884 TT
131 TT
* *
53360886 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCTAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
53360951 TCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCCACCATCTTCGATCTGCTCCAC-ATCTG
66 TCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCCGCTA-CTG
53361015 CTT
130 CTT
* * ** *
53361018 AAGGAGATAAGATCTGAAATCTTCAATCTATTCTACTGTTACCCAGGGAAGTAGAACTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* * *
53361083 TCAATGTACTCCACTATAACCACAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTATTGC
66 TCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCCGCTACTGC
53361148 TT
131 TT
* * * *
53361150 AGGGAGATAAAATCTGAAATCTTCAATATATTCCACTGTTGTCCAAGAAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* * * **
53361215 TCAATGTACTCCATTGTAACCACAGAGAGGTAAAATCCGCCACCTTCGATCTGCTTCGCTACTAA
66 TCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCCGCTACTGC
53361280 TT
131 TT
53361282 AGGGAGATAAGATCTG
1 AGGGAGATAAGATCTG
53361298 GAGTCTTCGA
Statistics
Matches: 489, Mismatches: 52, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
131 1 0.00
132 485 0.99
133 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCCGCTACTGC
TT
Found at i:53362670 original size:14 final size:15
Alignment explanation
Indices: 53362646--53362674 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53362636 AGCCTCTCCT
53362646 TTTTCTTTTTCTTTG
1 TTTTCTTTTTCTTTG
53362661 TTTT-TTTTTCTTTG
1 TTTTCTTTTTCTTTG
53362675 CTATTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTTCTTTG
Found at i:53367650 original size:50 final size:50
Alignment explanation
Indices: 53367595--53367750 Score: 128
Period size: 50 Copynumber: 3.2 Consensus size: 50
53367585 AAAGAAAATA
*
53367595 TACATATAGAAATTATAAAATGTGGATAGAAAATATAATACATATATACG
1 TACATATAGAAATTATAAAATATGGATAGAAAATATAATACATATATACG
* * * * *
53367645 TACATATATATAAGTTAATAAACATATAGATCA-TAAAGATAAT-GAT-TATA--
1 TACATATAGA-AA-TT-ATAAA-ATATGGAT-AGAAAATATAATACATATATACG
* * * *
53367695 TATATATAGAAATTATAAAATATGTATAGAAAGTAT--TATATATATACG
1 TACATATAGAAATTATAAAATATGGATAGAAAATATAATACATATATACG
53367743 TACATATA
1 TACATATA
53367751 TATATAAGGT
Statistics
Matches: 81, Mismatches: 15, Indels: 22
0.69 0.13 0.19
Matches are distributed among these distances:
44 1 0.01
45 3 0.04
46 14 0.17
47 5 0.06
48 9 0.11
49 2 0.02
50 17 0.21
51 2 0.02
52 6 0.07
53 7 0.09
54 14 0.17
55 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (50 bp):
TACATATAGAAATTATAAAATATGGATAGAAAATATAATACATATATACG
Found at i:53367713 original size:100 final size:99
Alignment explanation
Indices: 53367592--53367800 Score: 285
Period size: 100 Copynumber: 2.1 Consensus size: 99
53367582 AATAAAGAAA
* *
53367592 ATATACATATAGAAATTATAAAATGTGGATAGAAAATATAATACATATATACGTAC-ATATATAT
1 ATATATATATAGAAATTATAAAATATGGATAGAAAATAT--TACATATATACGTACAATATATAT
* * * *
53367656 AAGTTAATAAACATATAGATCATAAAGATAATGATT
64 AAGGTAATAAACATATAAATCATAAAAATAATAATT
* * *
53367692 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATTATATATATACGTACATATATATATA
1 ATATATATATAGAAATTATAAAATATGGATAGAAAATATTACATATATACGTACA-ATATATATA
*
53367757 AGGTAATAAATATATAAATCATAAAAATAATAATT
65 AGGTAATAAACATATAAATCATAAAAATAATAATT
*
53367792 ACATATATA
1 ATATATATA
53367801 AACTTAAAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
98 14 0.15
100 82 0.85
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (99 bp):
ATATATATATAGAAATTATAAAATATGGATAGAAAATATTACATATATACGTACAATATATATAA
GGTAATAAACATATAAATCATAAAAATAATAATT
Found at i:53367737 original size:20 final size:20
Alignment explanation
Indices: 53367689--53367740 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
53367679 AAAGATAATG
*
53367689 ATTATATATATATAGAAATT
1 ATTATATATATATAGAAAGT
* * *
53367709 ATAAAATATGTATAGAAAGT
1 ATTATATATATATAGAAAGT
53367729 ATTATATATATA
1 ATTATATATATA
53367741 CGTACATATA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (20 bp):
ATTATATATATATAGAAAGT
Found at i:53368976 original size:20 final size:19
Alignment explanation
Indices: 53368951--53369016 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
53368941 CTTGTTTACA
53368951 TTGATTTGATTCTCAATCTT
1 TTGATTTGATTCTCAATC-T
** * *
53368971 TTGATTTCTTTC-CATTACA
1 TTGATTTGATTCTCAAT-CT
53368990 TTGATTTGATTCTCAATCCT
1 TTGATTTGATTCTCAAT-CT
53369010 TTGATTT
1 TTGATTT
53369017 CTTTCTATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTGATTTGATTCTCAATCT
Found at i:53369000 original size:39 final size:39
Alignment explanation
Indices: 53368946--53369027 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
53368936 AAAATCTTGT
*
53368946 TTACATTGATTTGATTCTCAATCTTTTGATTTCTTTCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
*
53368985 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCTA
1 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
53369024 TTAC
1 TTAC
53369028 TGTTTTGCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.21, C:0.18, G:0.07, T:0.54
Consensus pattern (39 bp):
TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
Found at i:53369022 original size:20 final size:20
Alignment explanation
Indices: 53368960--53369022 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
53368950 ATTGATTTGA
*
53368960 TTCTCAATCTTTTGATTTCT
1 TTCTCAATCCTTTGATTTCT
* * * **
53368980 TTC-CATTACATTGATTTGA
1 TTCTCAATCCTTTGATTTCT
53368999 TTCTCAATCCTTTGATTTCT
1 TTCTCAATCCTTTGATTTCT
53369019 TTCT
1 TTCT
53369023 ATTACTGTTT
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.17, C:0.21, G:0.06, T:0.56
Consensus pattern (20 bp):
TTCTCAATCCTTTGATTTCT
Found at i:53372141 original size:11 final size:11
Alignment explanation
Indices: 53372125--53372150 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53372115 ATATATATTC
53372125 ATTTATTTATA
1 ATTTATTTATA
53372136 ATTTATTTATA
1 ATTTATTTATA
53372147 ATTT
1 ATTT
53372151 TGTATGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTATTTATA
Found at i:53372216 original size:18 final size:18
Alignment explanation
Indices: 53372174--53372216 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
53372164 ATTGAAAAAT
* *
53372174 GAATGTTTAAATATTTTT
1 GAATTTTTAAATATTTTA
* *
53372192 TATTTTTTAAATATTTTA
1 GAATTTTTAAATATTTTA
53372210 GAATTTT
1 GAATTTT
53372217 AATTTTAGAA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
GAATTTTTAAATATTTTA
Found at i:53372463 original size:29 final size:30
Alignment explanation
Indices: 53372394--53372466 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
53372384 TATTTAACAG
**
53372394 ATGAGTGACTAAAATATTAAATTTCGAAAAT
1 ATGAGTGACTAAAATAAAAAATTTC-AAAAT
* * *
53372425 ATTATTGACTAAAATAAAAAATTT-TAAAT
1 ATGAGTGACTAAAATAAAAAATTTCAAAAT
53372454 ATGAGTGACTAAA
1 ATGAGTGACTAAA
53372467 GCAGAAACGT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 15 0.43
31 20 0.57
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33
Consensus pattern (30 bp):
ATGAGTGACTAAAATAAAAAATTTCAAAAT
Found at i:53375711 original size:27 final size:27
Alignment explanation
Indices: 53375651--53375711 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
53375641 TTTTCATTCG
*
53375651 AATTCAATTTAAATAATAAAAAAATATT
1 AATT-AATTTAAATAATAAAAAAATATC
** * *
53375679 TTTTAATTTAAATTATAAAAACATATC
1 AATTAATTTAAATAATAAAAAAATATC
53375706 AATTAA
1 AATTAA
53375712 AAATTAAGGT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTAATTTAAATAATAAAAAAATATC
Found at i:53389432 original size:18 final size:17
Alignment explanation
Indices: 53389409--53389443 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
53389399 GTTGGGCCGA
53389409 AATGGGCCGTGTGGGCCC
1 AATGGG-CGTGTGGGCCC
*
53389427 AATGGGCTTGTGGGCCC
1 AATGGGCGTGTGGGCCC
53389444 CACATGGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.11, C:0.26, G:0.43, T:0.20
Consensus pattern (17 bp):
AATGGGCGTGTGGGCCC
Found at i:53390874 original size:18 final size:18
Alignment explanation
Indices: 53390848--53390882 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53390838 TTTCTTGTTG
*
53390848 TTTCTACTGTTTTTGCCA
1 TTTCCACTGTTTTTGCCA
53390866 TTTCCACTGTTTTTGCC
1 TTTCCACTGTTTTTGCC
53390883 CTCTGTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.26, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTCCACTGTTTTTGCCA
Found at i:53393487 original size:26 final size:25
Alignment explanation
Indices: 53393419--53393513 Score: 70
Period size: 26 Copynumber: 3.8 Consensus size: 25
53393409 TAAGATATAC
** **
53393419 AAAAATATGTATGTACGTGCAT-AT
1 AAAAATATGTATGTATATAAATAAT
* *
53393443 AAAAATATATATACT-TATAAA-AAT
1 AAAAATATGTAT-GTATATAAATAAT
53393467 AAAAGGATATGTATGTATATAAATTAAT
1 AAAA--ATATGTATGTATATAAA-TAAT
*
53393495 AATAATATGTATGTATATA
1 AAAAATATGTATGTATATA
53393514 CGGATTTATA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
24 19 0.35
25 2 0.04
26 28 0.51
28 6 0.11
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.36
Consensus pattern (25 bp):
AAAAATATGTATGTATATAAATAAT
Found at i:53395318 original size:44 final size:44
Alignment explanation
Indices: 53395227--53395326 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 44
53395217 ACTAGATGTG
* * * *
53395227 ATCTGCTCCACTGTAATCTCAGAGAGATAAGATCTCTGGCTTCA
1 ATCTGCTCCACTGTAACCTCAGAAAGATAAGATCTCTGGCCTAA
*
53395271 ATCTGCTCCACTGTAACCTCAGAAAGATAAGA-CTGGTGGCCTAA
1 ATCTGCTCCACTGTAACCTCAGAAAGATAAGATCT-CTGGCCTAA
*
53395315 ATCTGCTTCACT
1 ATCTGCTCCACT
53395327 ACTGCTTAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 2 0.04
44 47 0.96
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
ATCTGCTCCACTGTAACCTCAGAAAGATAAGATCTCTGGCCTAA
Found at i:53395362 original size:44 final size:44
Alignment explanation
Indices: 53395314--53395598 Score: 261
Period size: 44 Copynumber: 6.5 Consensus size: 44
53395304 TGGTGGCCTA
* * * *
53395314 AATCTGCTTCACTACTGCTTAGGAAGATAAGAT-TCGCCGTCTTC
1 AATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-ACCATCTTC
* *
53395358 AATCTTCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTT
1 AATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTC
* * * *
53395402 GACCTGCTCCAC-ACTGCTTAGGGAGATAGGATCTACCATCTTT
1 AATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTC
* * * *
53395445 GACCTGCTCCACTACTACTTAGGGAGATAGGATCTACCATCTTC
1 AATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTC
* * * **** *
53395489 GACCTGCTCCACTACTGCTTAGGGAGATAGGA-CTAGTGGCTTA
1 AATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTC
* * * * * * *
53395532 AATCTGCTTCACTATTGCTTAGGAAGATAATATTTGCCCTCTTC
1 AATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTC
* *
53395576 AATCTGCTCCACTAGTACTTAGG
1 AATCTGCTCCACTACTGCTTAGG
53395599 AAGGCAAGAT
Statistics
Matches: 203, Mismatches: 35, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
43 73 0.36
44 129 0.64
45 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTC
Found at i:53395428 original size:43 final size:44
Alignment explanation
Indices: 53395364--53395520 Score: 280
Period size: 44 Copynumber: 3.6 Consensus size: 44
53395354 CTTCAATCTT
*
53395364 CTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTTGACCTG
1 CTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGACCTG
53395408 CTCCAC-ACTGCTTAGGGAGATAGGATCTACCATCTTTGACCTG
1 CTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGACCTG
* *
53395451 CTCCACTACTACTTAGGGAGATAGGATCTACCATCTTCGACCTG
1 CTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGACCTG
53395495 CTCCACTACTGCTTAGGGAGATAGGA
1 CTCCACTACTGCTTAGGGAGATAGGA
53395521 CTAGTGGCTT
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
43 42 0.39
44 66 0.61
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGACCTG
Found at i:53395539 original size:87 final size:87
Alignment explanation
Indices: 53395317--53395598 Score: 287
Period size: 87 Copynumber: 3.2 Consensus size: 87
53395307 TGGCCTAAAT
* * * * * * *
53395317 CTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCAATCTTCTCCACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTAG-CGTCTTAAATCTGCTCCACTACTGCTTAGGG
*
53395382 AGATAAGATCTACCATCTTTGAC
65 AGATAAGATCTACCATCTTCGAC
* * ** * *
53395405 CTGCTCCAC-ACTGCTTAGGGAGATAGGATCTACCATCTTTGACCTGCTCCACTACTACTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGA-CTAGCGTCTTAAATCTGCTCCACTACTGCTTAGGG
*
53395469 AGATAGGATCTACCATCTTCGAC
65 AGATAAGATCTACCATCTTCGAC
* * * * *
53395492 CTGCTCCACTACTGCTTAGGGAGATAGGACTAGTGGCTTAAATCTGCTTCACTATTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTAGCGTCTTAAATCTGCTCCACTACTGCTTAGGGA
* * * * * *
53395557 GATAATATTTGCCCTCTTCAAT
66 GATAAGATCTACCATCTTCGAC
* *
53395579 CTGCTCCACTAGTACTTAGG
1 CTGCTCCACTACTGCTTAGG
53395599 AAGGCAAGAT
Statistics
Matches: 158, Mismatches: 34, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
87 130 0.82
88 28 0.18
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (87 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGACTAGCGTCTTAAATCTGCTCCACTACTGCTTAGGGA
GATAAGATCTACCATCTTCGAC
Found at i:53395816 original size:86 final size:86
Alignment explanation
Indices: 53395577--53396386 Score: 1141
Period size: 86 Copynumber: 9.4 Consensus size: 86
53395567 GCCCTCTTCA
* *
53395577 ATCTGCTCCACTAGTACTTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
1 ATCTGCTCCATTAGTACTTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGAT
* *
53395642 GGAGGTAAGGCTTTGTTTTCG
66 GGAGGCAAGGCTTTGTTTTTG
* ** * *
53395663 ATCTGCTTCGCTGTTA--ACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACC
1 ATCTGC-TC-C-ATTAGTACTTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACA
* *
53395726 GATGGAGGTAAGGCTTTGTTTTCG
63 GATGGAGGCAAGGCTTTGTTTTTG
*
53395750 ATCTGCTCCGTTAGTACTTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGAT
1 ATCTGCTCCATTAGTACTTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGAT
53395815 GGAGGCAAGGCTTTGTTTTTG
66 GGAGGCAAGGCTTTGTTTTTG
* *
53395836 ATCTGCTCCATTAGTACTTAGGAATGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACAGAT
1 ATCTGCTCCATTAGTACTTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGAT
53395901 GGAGGCAAGGCTTTGTTTTTG
66 GGAGGCAAGGCTTTGTTTTTG
* *
53395922 ATCTGCTCCATTAGTACTTAGGAATGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACAGAT
1 ATCTGCTCCATTAGTACTTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGAT
53395987 GGAGGCAAGGCTTTGTTTTTG
66 GGAGGCAAGGCTTTGTTTTTG
* *
53396008 ATCTGCTCCATTAGTACTTAGGAATGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACAGAT
1 ATCTGCTCCATTAGTACTTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGAT
* * *
53396073 GGAGGTAGGGCTTTGTTTTTT
66 GGAGGCAAGGCTTTGTTTTTG
*
53396094 ATCTGCTCC-TCTAGTACTTAGGAAGGCAATATCTGCTATCTTTAACCAGCTCCACTGCAACAGA
1 ATCTGCTCCAT-TAGTACTTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGA
* * *
53396158 TGGAGGTAGGGCTTTGTTTTTT
65 TGGAGGCAAGGCTTTGTTTTTG
* *
53396180 ATCTGCTCC-TCTAGTACTTAGGAAGGCAATATCTGCTATCTTTAACCAGCTCCACTGCAACCGA
1 ATCTGCTCCAT-TAGTACTTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGA
**
53396244 TGGAGGCAAGGCTTTGTTTTCA
65 TGGAGGCAAGGCTTTGTTTTTG
* * * * *
53396266 ATCTGCTTCGCTGTTAATGC--AGGAAGGCAAGATCTGCT-TCTTTAACCAGCTTCACTGCAACC
1 ATCTGC-TC-C-ATTAGTACTTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACA
53396328 GATGGAGGCAAGGCTTTGTTTTTG
63 GATGGAGGCAAGGCTTTGTTTTTG
* * *
53396352 ATCTGCTTCGTT-GTTAATGTAGGAAGGCAAGATCT
1 ATCTGCTCCATTAG-TACT-TAGGAAGGCAAGATCT
53396387 ACTTTTTTTT
Statistics
Matches: 675, Mismatches: 35, Indels: 28
0.91 0.05 0.04
Matches are distributed among these distances:
83 4 0.01
84 5 0.01
85 3 0.00
86 559 0.83
87 95 0.14
88 2 0.00
89 6 0.01
90 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (86 bp):
ATCTGCTCCATTAGTACTTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGAT
GGAGGCAAGGCTTTGTTTTTG
Found at i:53395865 original size:42 final size:42
Alignment explanation
Indices: 53395819--53396037 Score: 140
Period size: 42 Copynumber: 5.1 Consensus size: 42
53395809 ACAGATGGAG
53395819 GCAAGGCTTTGTTTTTGATCTGCTCCATTAGTACTTAGGAAT
1 GCAAGGCTTTGTTTTTGATCTGCTCCATTAGTACTTAGGAAT
* * * * * * * * ** *
53395861 GCAAGATCTGTTATCTTTAACCAGCTCCACT-GCAACAGATGG-AG
1 GCAAG-GCT-TTGTTTTTGATCTGCTCCATTAG-TACTTA-GGAAT
53395905 GCAAGGCTTTGTTTTTGATCTGCTCCATTAGTACTTAGGAAT
1 GCAAGGCTTTGTTTTTGATCTGCTCCATTAGTACTTAGGAAT
* * * * * * * * ** *
53395947 GCAAGATCTGTTATCTTTAACCAGCTCCACT-GCAACAGATGG-AG
1 GCAAG-GCT-TTGTTTTTGATCTGCTCCATTAG-TACTTA-GGAAT
53395991 GCAAGGCTTTGTTTTTGATCTGCTCCATTAGTACTTAGGAAT
1 GCAAGGCTTTGTTTTTGATCTGCTCCATTAGTACTTAGGAAT
53396033 GCAAG
1 GCAAG
53396038 ATCTGTTATC
Statistics
Matches: 121, Mismatches: 44, Indels: 24
0.64 0.23 0.13
Matches are distributed among these distances:
41 4 0.03
42 53 0.44
43 12 0.10
44 48 0.40
45 4 0.03
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (42 bp):
GCAAGGCTTTGTTTTTGATCTGCTCCATTAGTACTTAGGAAT
Found at i:53396295 original size:43 final size:43
Alignment explanation
Indices: 53396247--53396382 Score: 109
Period size: 43 Copynumber: 3.2 Consensus size: 43
53396237 CAACCGATGG
*
53396247 AGGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGCTTTGTTTTTAATCTGCTTCGCTGTTAATGCAGGA
* * * * * * *
53396290 AGGCAA-GATCTGCTTCTTTAACCAGCTTCACTG-CAA-CCGATGG-
1 AGGCAAGGCTTTG-TT-TTTAATCTGCTTCGCTGTTAATGC-A-GGA
* * *
53396333 AGGCAAGGCTTTGTTTTTGATCTGCTTCGTTGTTAATGTAGGA
1 AGGCAAGGCTTTGTTTTTAATCTGCTTCGCTGTTAATGCAGGA
53396376 AGGCAAG
1 AGGCAAG
53396383 ATCTACTTTT
Statistics
Matches: 67, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
42 19 0.28
43 29 0.43
44 19 0.28
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (43 bp):
AGGCAAGGCTTTGTTTTTAATCTGCTTCGCTGTTAATGCAGGA
Found at i:53404391 original size:74 final size:74
Alignment explanation
Indices: 53404171--53404384 Score: 378
Period size: 74 Copynumber: 2.9 Consensus size: 74
53404161 TAAATAATAA
*
53404171 TTAAGTTGGATGTTATGGTGAGTGATGTAAAATGTCACAAAAGTATATAAAAATGCAATTATTAC
1 TTAAGTTGTATGTTATGGTGAGTGATGTAAAATGTCACAAAAGTATATAAAAATGCAATTATTAC
53404236 TGATTTTAG
66 TGATTTTAG
53404245 TTAAGTTGTATGTTATGGTGAGTGATGTAAAATGTCACAAAAGTATATAAAAATGCAATTATTAC
1 TTAAGTTGTATGTTATGGTGAGTGATGTAAAATGTCACAAAAGTATATAAAAATGCAATTATTAC
53404310 TGATTTTAG
66 TGATTTTAG
*
53404319 TTAAGTTGTATGTTATGGTGAGTGATGTAAAATGTCAC-AAAGTAATATAAGAGA-GCAATTATT
1 TTAAGTTGTATGTTATGGTGAGTGATGTAAAATGTCACAAAAGT-ATATAA-AAATGCAATTATT
53404382 ACT
64 ACT
53404385 AGTTTTAATG
Statistics
Matches: 136, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
73 5 0.04
74 129 0.95
75 2 0.01
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (74 bp):
TTAAGTTGTATGTTATGGTGAGTGATGTAAAATGTCACAAAAGTATATAAAAATGCAATTATTAC
TGATTTTAG
Found at i:53412521 original size:24 final size:23
Alignment explanation
Indices: 53412487--53412555 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 23
53412477 AACCCGACCC
53412487 ATAT-TAAATATATATATTTAAT
1 ATATATAAATATATATATTTAAT
* *
53412509 ATATAT-AATATATAT-TTGATT
1 ATATATAAATATATATATTTAAT
* * *
53412530 AAAAATAAAAATATATATTTAAT
1 ATATATAAATATATATATTTAAT
53412553 ATA
1 ATA
53412556 AAATTTGGGC
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
21 8 0.22
22 21 0.58
23 7 0.19
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (23 bp):
ATATATAAATATATATATTTAAT
Found at i:53412558 original size:24 final size:24
Alignment explanation
Indices: 53412491--53412559 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
53412481 CGACCCATAT
*
53412491 TAAATATATATATTTAATAT---A
1 TAAAAATATATATTTAATATAAAA
* *
53412512 T-ATAATATATATTTGAT-TAAAAA
1 TAAAAATATATATTTAATAT-AAAA
53412535 TAAAAATATATATTTAATATAAAA
1 TAAAAATATATATTTAATATAAAA
53412559 T
1 T
53412560 TTGGGCCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
19 1 0.03
20 13 0.35
21 1 0.03
23 2 0.05
24 19 0.51
25 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (24 bp):
TAAAAATATATATTTAATATAAAA
Found at i:53412945 original size:26 final size:25
Alignment explanation
Indices: 53412881--53412955 Score: 60
Period size: 26 Copynumber: 2.8 Consensus size: 25
53412871 ATTTTTTAAT
* **
53412881 TATTTTAAAGAAATAGAAAATGAAAGC
1 TATTTTAAA-AAATA-AAAATAAAAAA
*
53412908 TATTTTTTAAAAATAAAAATAAAAAA
1 TA-TTTTAAAAAATAAAAATAAAAAA
* *
53412934 TATTTTCAAAAACTAAACATAA
1 TATTTT-AAAAAATAAAAATAA
53412956 CCTAAAATTC
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
25 4 0.10
26 22 0.56
27 7 0.18
28 6 0.15
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (25 bp):
TATTTTAAAAAATAAAAATAAAAAA
Found at i:53428601 original size:19 final size:19
Alignment explanation
Indices: 53428573--53428618 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
53428563 GATCGAAGGT
53428573 GGATCGGTGGACTGGAGGA
1 GGATCGGTGGACTGGAGGA
*
53428592 GGATCTGTGGACTGGAGGA
1 GGATCGGTGGACTGGAGGA
53428611 GGATCGGT
1 GGATCGGT
53428619 ATTTTGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.11, G:0.50, T:0.20
Consensus pattern (19 bp):
GGATCGGTGGACTGGAGGA
Found at i:53429767 original size:27 final size:27
Alignment explanation
Indices: 53429717--53429828 Score: 156
Period size: 27 Copynumber: 4.1 Consensus size: 27
53429707 GGGTATAACA
*
53429717 GTCATTTTACCCTATGAGAGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
53429744 GTCATTTTACCCTATG-GGGTTATTTTG
1 GTCATTTTACCCTATGAGGG-TATTTCG
53429771 GTCATTTTACCCTATGAGGGTA-TTCTG
1 GTCATTTTACCCTATGAGGGTATTTC-G
* *
53429798 GTCATTTTACCTTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
53429825 GTCA
1 GTCA
53429829 GATATCGACC
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.05
27 66 0.87
28 6 0.08
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:53429787 original size:54 final size:54
Alignment explanation
Indices: 53429717--53429828 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
53429707 GGGTATAACA
* *
53429717 GTCATTTTACCCTATGAGAGTATT-TCGGTCATTTTACCCTATGGGGTTATTTTG
1 GTCATTTTACCCTATGAGAGTATTCT-GGTCATTTTACCCTATGGGGGTATTTCG
* *
53429771 GTCATTTTACCCTATGAGGGTATTCTGGTCATTTTACCTTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGAGTATTCTGGTCATTTTACCCTATGGGGGTATTTCG
53429825 GTCA
1 GTCA
53429829 GATATCGACC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 52 0.98
55 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43
Consensus pattern (54 bp):
GTCATTTTACCCTATGAGAGTATTCTGGTCATTTTACCCTATGGGGGTATTTCG
Found at i:53432354 original size:39 final size:39
Alignment explanation
Indices: 53432150--53432372 Score: 182
Period size: 40 Copynumber: 5.6 Consensus size: 39
53432140 TTGAATGCTG
* * * * *
53432150 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
53432190 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
53432229 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* * * *
53432270 TCGGGGTTAAGTCCCGAAGGCATTCATGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
53432310 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * * *
53432349 ACCGGGCTATGTCTCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
53432373 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 23, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
39 38 0.25
40 100 0.66
41 13 0.09
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:53435997 original size:98 final size:98
Alignment explanation
Indices: 53435828--53436019 Score: 321
Period size: 98 Copynumber: 2.0 Consensus size: 98
53435818 AATAAAAATA
*
53435828 TTAAAAGAACATCCACTCATCCAAAATTTAAGAAACCACACCCAATACGTTAGGGCACGATTCCT
1 TTAAAAGAACATCCACTCATCCAAAATTTAAGAAACCACACCCAATACGTTAGGGCACAATTCCT
*
53435893 TTAGAATCCCGAACTCAGAATATTTCCTTTAAT
66 TTAGAATCCCAAACTCAGAATATTTCCTTTAAT
* * *
53435926 TTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCCT
1 TTAAAAGAACATCCACTCATCCAAAATTTAAGAAACCACACCCAATACGTTAGGGCACAATTCCT
* *
53435991 TTAGAATCTCAAACTCGGAATATTTCCTT
66 TTAGAATCCCAAACTCAGAATATTTCCTT
53436020 CATGATTTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (98 bp):
TTAAAAGAACATCCACTCATCCAAAATTTAAGAAACCACACCCAATACGTTAGGGCACAATTCCT
TTAGAATCCCAAACTCAGAATATTTCCTTTAAT
Found at i:53438128 original size:41 final size:41
Alignment explanation
Indices: 53438071--53438157 Score: 174
Period size: 41 Copynumber: 2.1 Consensus size: 41
53438061 AAATTATTCT
53438071 TGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAAC
1 TGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAAC
53438112 TGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAAC
1 TGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAAC
53438153 TGAAT
1 TGAAT
53438158 TAGACTTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.21
Consensus pattern (41 bp):
TGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAAC
Found at i:53438173 original size:41 final size:41
Alignment explanation
Indices: 53438071--53438173 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
53438061 AAATTATTCT
* *
53438071 TGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAAC
1 TGAATCAGACTATAAACCTAGCAGGCTAAGTGCCGGTGAAC
* *
53438112 TGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAAC
1 TGAATCAGACTATAAACCTAGCAGGCTAAGTGCCGGTGAAC
* *
53438153 TGAATTAGACTTTAAACCTAG
1 TGAATCAGACTATAAACCTAG
53438174 TAGATGAAGT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.22
Consensus pattern (41 bp):
TGAATCAGACTATAAACCTAGCAGGCTAAGTGCCGGTGAAC
Found at i:53441277 original size:44 final size:44
Alignment explanation
Indices: 53441229--53441451 Score: 152
Period size: 44 Copynumber: 5.1 Consensus size: 44
53441219 TATCTTGGAA
*
53441229 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * *
53441273 AGATAAGA-TCTTCAATCTTCAACCTTCTCCACTACTGCTCAGGG
1 AGATAAGATTC-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * *
53441317 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
53441361 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * *
53441405 AGATAAGA-TCTACAATCTTCAACCTTCTCCACTACTACTTAGGG
1 AGATAAGATTC-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
53441449 AGA
1 AGA
53441452 CAAGGCTTGG
Statistics
Matches: 134, Mismatches: 34, Indels: 22
0.71 0.18 0.12
Matches are distributed among these distances:
42 6 0.04
43 11 0.08
44 105 0.78
45 5 0.04
46 7 0.05
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (44 bp):
AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:53441412 original size:132 final size:132
Alignment explanation
Indices: 53441175--53441463 Score: 533
Period size: 132 Copynumber: 2.2 Consensus size: 132
53441165 NNNNNNACTG
*
53441175 CTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTTCCACTATCTTGGAAAGATAAGATTC
1 CTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTC
* *
53441240 GCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCAC
66 ACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCAC
53441305 TA
131 TA
53441307 CTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTC
1 CTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTC
53441372 ACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCAC
66 ACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCAC
53441437 TA
131 TA
* *
53441439 CTACTTAGGGAGACAAGGCTTGGTG
1 CTGCTCAGGGAGACAAGGCTTGGTG
53441464 TTTCACCAAT
Statistics
Matches: 152, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 152 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (132 bp):
CTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTC
ACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCAC
TA
Found at i:53445898 original size:22 final size:22
Alignment explanation
Indices: 53445873--53445916 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53445863 AATTTTCACC
*
53445873 TCTTTCCCTTCTTCCAGGCTCA
1 TCTTTCCCTTCCTCCAGGCTCA
53445895 TCTTTCCCTTCCTCCAGGCTCA
1 TCTTTCCCTTCCTCCAGGCTCA
53445917 CAACTTCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.43, G:0.09, T:0.39
Consensus pattern (22 bp):
TCTTTCCCTTCCTCCAGGCTCA
Found at i:53453098 original size:98 final size:98
Alignment explanation
Indices: 53452929--53453120 Score: 321
Period size: 98 Copynumber: 2.0 Consensus size: 98
53452919 AATAAAAATA
*
53452929 TTAAAAGAACATCCACTCATCCAAAATTTAAGAAACCACACCCAATACGTTAGGGCACGATTCCT
1 TTAAAAGAACATCCACTCATCCAAAATTTAAGAAACCACACCCAATACGTTAGGGCACAATTCCT
*
53452994 TTAGAATCCCGAACTCAGAATATTTCCTTTAAT
66 TTAGAATCCCAAACTCAGAATATTTCCTTTAAT
* * *
53453027 TTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCCT
1 TTAAAAGAACATCCACTCATCCAAAATTTAAGAAACCACACCCAATACGTTAGGGCACAATTCCT
* *
53453092 TTAGAATCTCAAACTCGGAATATTTCCTT
66 TTAGAATCCCAAACTCAGAATATTTCCTT
53453121 CATGATTTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (98 bp):
TTAAAAGAACATCCACTCATCCAAAATTTAAGAAACCACACCCAATACGTTAGGGCACAATTCCT
TTAGAATCCCAAACTCAGAATATTTCCTTTAAT
Found at i:53454309 original size:20 final size:20
Alignment explanation
Indices: 53454278--53454333 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
53454268 GAATTTCTTG
53454278 TAAAAGATAATAATATTTTAA
1 TAAAA-ATAATAATATTTTAA
*
53454299 TAAAAATAATAAAATTTTAA
1 TAAAAATAATAATATTTTAA
53454319 TAGGAAAATAA-AATA
1 TA--AAAATAATAATA
53454334 AAAAGATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.52
21 8 0.26
22 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAAAATAATAATATTTTAA
Found at i:53454429 original size:21 final size:22
Alignment explanation
Indices: 53454386--53454433 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
53454376 GTTAATTGGA
53454386 AAATATATATCAAATTATAAAAT
1 AAATATATATCAAA-TATAAAAT
* *
53454409 AAATATATTTCAAA-ATTAAAT
1 AAATATATATCAAATATAAAAT
53454430 AAAT
1 AAAT
53454434 TGTTTTAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
23 13 0.57
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATATATATCAAATATAAAAT
Found at i:53456114 original size:18 final size:18
Alignment explanation
Indices: 53456091--53456125 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53456081 GCTGTGTAAG
*
53456091 CCACACGAGCGTGTGGGC
1 CCACACGAGCATGTGGGC
*
53456109 CCACACGGGCATGTGGG
1 CCACACGAGCATGTGGG
53456126 ATTATTGGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.31, G:0.40, T:0.11
Consensus pattern (18 bp):
CCACACGAGCATGTGGGC
Found at i:53463716 original size:17 final size:18
Alignment explanation
Indices: 53463694--53463728 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
53463684 TGAATTGAGC
53463694 CGTGTGGGCC-ACACGAG
1 CGTGTGGGCCTACACGAG
53463711 CGTGTGGGCCTACACGAG
1 CGTGTGGGCCTACACGAG
53463729 TGAACCATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.17, C:0.29, G:0.40, T:0.14
Consensus pattern (18 bp):
CGTGTGGGCCTACACGAG
Found at i:53465496 original size:13 final size:15
Alignment explanation
Indices: 53465476--53465512 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
53465466 TTTTTGATTA
53465476 ACTAAAAAA-TAAGT
1 ACTAAAAAATTAAGT
53465490 A-TAAAAAATTTAAGT
1 ACTAAAAAA-TTAAGT
53465505 ACTAAAAA
1 ACTAAAAA
53465513 TTTTGTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.35
14 1 0.05
15 6 0.30
16 6 0.30
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (15 bp):
ACTAAAAAATTAAGT
Found at i:53466239 original size:28 final size:28
Alignment explanation
Indices: 53466207--53466272 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
53466197 ACTGTTCATT
53466207 GTTGGGTGACAAAA-AAATTTAACTAATA
1 GTTGGGTGACAAAATAAATTT-ACTAATA
53466235 GTTGGGTGACAAAATAAATTTACTAATA
1 GTTGGGTGACAAAATAAATTTACTAATA
*
53466263 GTTAGGTGAC
1 GTTGGGTGAC
53466273 TATTAGTGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 30 0.83
29 6 0.17
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (28 bp):
GTTGGGTGACAAAATAAATTTACTAATA
Found at i:53466660 original size:18 final size:18
Alignment explanation
Indices: 53466637--53466696 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
53466627 ATTTAACTTT
53466637 AATTAAATTACTTAAAAC
1 AATTAAATTACTTAAAAC
** ***
53466655 AATT-AATTTTTTAATTTT
1 AATTAAATTACTTAA-AAC
*
53466673 AATTAAATTACTTAAGAC
1 AATTAAATTACTTAAAAC
53466691 AATTAA
1 AATTAA
53466697 TTTTTTAAAT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
17 8 0.27
18 14 0.47
19 8 0.27
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (18 bp):
AATTAAATTACTTAAAAC
Found at i:53466675 original size:36 final size:36
Alignment explanation
Indices: 53466628--53466704 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
53466618 ATCTTCTTAA
53466628 TTTAACTTTAATTAAATTACTTAAAACAATTAATTT
1 TTTAACTTTAATTAAATTACTTAAAACAATTAATTT
* *
53466664 TTTAATTTTAATTAAATTACTTAAGACAATTAATTT
1 TTTAACTTTAATTAAATTACTTAAAACAATTAATTT
53466700 TTTAA
1 TTTAA
53466705 ATTATAAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.49
Consensus pattern (36 bp):
TTTAACTTTAATTAAATTACTTAAAACAATTAATTT
Done.