Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 156 of 163
Found at i:43663188 original size:2 final size:2
Alignment explanation
Indices: 43663183--43663209 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43663173 ATATATATAT
43663183 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
43663210 ACCCAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:43667298 original size:38 final size:38
Alignment explanation
Indices: 43667242--43667322 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
43667232 AAACTGCTAA
* *
43667242 GAAATTCTAGAATTACATGCCTTATTTACAAACAGTGT
1 GAAATTCTAGAATAACATGCCTTAATTACAAACAGTGT
43667280 GAAATTCTAGAATAACATGCCTTAATTACAAACAGTGT
1 GAAATTCTAGAATAACATGCCTTAATTACAAACAGTGT
*
43667318 TAAAT
1 GAAAT
43667323 CTCAGGAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (38 bp):
GAAATTCTAGAATAACATGCCTTAATTACAAACAGTGT
Found at i:43672219 original size:28 final size:29
Alignment explanation
Indices: 43672148--43672230 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 29
43672138 TTATTATTGT
*
43672148 ATTAATTTATAATTTTATAATTATTAAAA
1 ATTAAATTATAATTTTATAATTATTAAAA
* * * *
43672177 ATT-AATTA-ATTTTTTATTATT-TTGAGA
1 ATTAAATTATA-ATTTTATAATTATTAAAA
*
43672204 ATTAAATTATAATTTTACAATTATTAA
1 ATTAAATTATAATTTTATAATTATTAA
43672231 CTTATAAATT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
27 8 0.20
28 26 0.63
29 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (29 bp):
ATTAAATTATAATTTTATAATTATTAAAA
Found at i:43675657 original size:21 final size:21
Alignment explanation
Indices: 43675633--43675672 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43675623 TATTATTACA
* *
43675633 TCAACGTTTTCATTTTAAATT
1 TCAACATTTTCATCTTAAATT
*
43675654 TCAATATTTTCATCTTAAA
1 TCAACATTTTCATCTTAAA
43675673 AAAAATCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.50
Consensus pattern (21 bp):
TCAACATTTTCATCTTAAATT
Found at i:43676726 original size:39 final size:39
Alignment explanation
Indices: 43676671--43676757 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
43676661 AAGAAAAGAA
43676671 GAATAAGCTGAAAATTTGACCCTCTGTTACTCAAACAAAG
1 GAAT-AGCTGAAAATTTGACCCTCTGTTACTCAAACAAAG
*
43676711 GAATAGCTGAAAATTTGACCCTCTGTTATTCAAACAAAG
1 GAATAGCTGAAAATTTGACCCTCTGTTACTCAAACAAAG
43676750 GAATAGCT
1 GAATAGCT
43676758 ATTATAATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 42 0.91
40 4 0.09
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (39 bp):
GAATAGCTGAAAATTTGACCCTCTGTTACTCAAACAAAG
Found at i:43676841 original size:26 final size:24
Alignment explanation
Indices: 43676812--43676896 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
43676802 AATCGAAATT
43676812 AAATTGTATATTTTTATAATTATAAA
1 AAATT-TATATTTTTATAATT-TAAA
* * * *
43676838 AAATATATAATTTTATTATTTTAA
1 AAATTTATATTTTTATAATTTAAA
* *
43676862 TAATTTATATATTTATAA---AAA
1 AAATTTATATTTTTATAATTTAAA
43676883 AAATTTATCATTTT
1 AAATTTAT-ATTTT
43676897 CTTGAGTTCA
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
21 9 0.20
22 4 0.09
24 16 0.35
25 13 0.28
26 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
AAATTTATATTTTTATAATTTAAA
Found at i:43677514 original size:16 final size:17
Alignment explanation
Indices: 43677469--43677511 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
43677459 GTAATCTAAC
*
43677469 TAAAAAATTT-TATGATA
1 TAAAAAATTTAT-TAATA
43677486 TAAAAAATTTATTAATA
1 TAAAAAATTTATTAATA
*
43677503 TGAAAAATT
1 TAAAAAATT
43677512 ATTGGTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (17 bp):
TAAAAAATTTATTAATA
Found at i:43684483 original size:17 final size:17
Alignment explanation
Indices: 43684450--43684483 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43684440 TAAAAAAATT
* *
43684450 ATAAAAATTGTTTTAAA
1 ATAAAAATTATTATAAA
43684467 ATAAAAATTATTATAAA
1 ATAAAAATTATTATAAA
43684484 CGTATAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAAAAATTATTATAAA
Found at i:43684776 original size:157 final size:161
Alignment explanation
Indices: 43684615--43684942 Score: 529
Period size: 165 Copynumber: 2.0 Consensus size: 161
43684605 TTTCTATTCA
*
43684615 TTATTGGGTAATTTGATAAATAATATAAGTTTAATAA-T-TAAAAAAATAAAATAAAAAATAAAA
1 TTATTGGATAATTTGATAAATAATATAAGTTTAATAATTATAAAAAAATAAAATAAAAAATAAAA
*
43684678 ATAATTTTTTATATAAAATTGAAGGATCAAATAAATCA-TTATA-TATATATATATATTGTGTTC
66 ATAATTTTTTATATAAAATTAAAGGATCAAATAAATCATTTATAGTATATATATATATTGTGTTC
43684741 GTTTCCTTTGTTTTCTTGATTTATGAGTTAC
131 GTTTCCTTTGTTTTCTTGATTTATGAGTTAC
43684772 TTATTGGATAATTTGATAAATAATATAAGTTTAATAATTAAAAAAATAAAAAAATAAAATAAAAA
1 TTATTGGATAATTTGATAAATAATATAAGTTTAATAATT------ATAAAAAAATAAAATAAAAA
*
43684837 ATTAAAATAATTTTTTATATAAAATTAAAGGATCAAATAAATCATTTTATATGTATATATATATA
60 ATAAAAATAATTTTTTATATAAAATTAAAGGATCAAATAAATCA-TTTATA-GTATATATATATA
43684902 TTGTGTTCGTTTCCTTTGTTTTCTTGATTTATGAGTTAC
123 TTGTGTTCGTTTCCTTTGTTTTCTTGATTTATGAGTTAC
43684941 TT
1 TT
43684943 TCACCTTAAA
Statistics
Matches: 156, Mismatches: 3, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
157 36 0.23
158 1 0.01
165 61 0.39
167 5 0.03
169 53 0.34
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (161 bp):
TTATTGGATAATTTGATAAATAATATAAGTTTAATAATTATAAAAAAATAAAATAAAAAATAAAA
ATAATTTTTTATATAAAATTAAAGGATCAAATAAATCATTTATAGTATATATATATATTGTGTTC
GTTTCCTTTGTTTTCTTGATTTATGAGTTAC
Found at i:43684832 original size:13 final size:13
Alignment explanation
Indices: 43684814--43684846 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
43684804 AATAATTAAA
43684814 AAAATAAAAAAAT
1 AAAATAAAAAAAT
*
43684827 AAAATAAAAAATT
1 AAAATAAAAAAAT
43684840 AAAATAA
1 AAAATAA
43684847 TTTTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:43687761 original size:21 final size:22
Alignment explanation
Indices: 43687710--43687761 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
43687700 ATTTTAATAA
* *
43687710 ATTATATGATAAAATAAATCTGT
1 ATTATA-GAAAAAATAAATCTCT
43687733 ATTATAGAAAAAATAAATCTCT
1 ATTATAGAAAAAATAAATCTCT
43687755 ATT-TAGA
1 ATTATAGA
43687762 CGGGGTGCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 4 0.15
22 17 0.63
23 6 0.22
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.37
Consensus pattern (22 bp):
ATTATAGAAAAAATAAATCTCT
Found at i:43688709 original size:6 final size:6
Alignment explanation
Indices: 43688698--43688727 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
43688688 TGTTAGATTG
43688698 AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA
43688728 TTGGGTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:43692629 original size:14 final size:15
Alignment explanation
Indices: 43692610--43692642 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
43692600 AGTTAGGACT
*
43692610 AAAATTTTAAA-TTA
1 AAAATTTAAAATTTA
43692624 AAAATTTAAAATTTA
1 AAAATTTAAAATTTA
43692639 AAAA
1 AAAA
43692643 AAGGTATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATTTAAAATTTA
Found at i:43705012 original size:54 final size:55
Alignment explanation
Indices: 43704928--43705043 Score: 189
Period size: 54 Copynumber: 2.1 Consensus size: 55
43704918 ATTTTCCTTG
*
43704928 TTGAAAAAAAAATAGTGGATTTTTTACACAAATAAATGGAAAACTTGCTCTCAAA
1 TTGAAAAAAAAATAGTGGAATTTTTACACAAATAAATGGAAAACTTGCTCTCAAA
* * *
43704983 TTGAAAAAAAAA-AGTGGAATTTTTGCACAAATAATTGGAAAACTTGCTCTCAAG
1 TTGAAAAAAAAATAGTGGAATTTTTACACAAATAAATGGAAAACTTGCTCTCAAA
43705037 TTGAAAA
1 TTGAAAA
43705044 TATTTTAGCC
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 45 0.79
55 12 0.21
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (55 bp):
TTGAAAAAAAAATAGTGGAATTTTTACACAAATAAATGGAAAACTTGCTCTCAAA
Found at i:43718363 original size:3 final size:3
Alignment explanation
Indices: 43718357--43718399 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
43718347 TTCTTAACAC
43718357 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
43718400 GCACTATGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:43719956 original size:2 final size:2
Alignment explanation
Indices: 43719941--43720013 Score: 119
Period size: 2 Copynumber: 36.0 Consensus size: 2
43719931 TTACAATAGT
*
43719941 TA TA TA GTA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
43719984 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43720014 ATTGAAGAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
2 64 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:43736817 original size:18 final size:18
Alignment explanation
Indices: 43736791--43736825 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43736781 GTCAGATTCA
*
43736791 GAAAGTGATGACGATGAG
1 GAAAATGATGACGATGAG
*
43736809 GAAAATGATGATGATGA
1 GAAAATGATGACGATGA
43736826 TGGCCAAAAG
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:0.43, C:0.03, G:0.34, T:0.20
Consensus pattern (18 bp):
GAAAATGATGACGATGAG
Found at i:43762180 original size:53 final size:53
Alignment explanation
Indices: 43762103--43762218 Score: 187
Period size: 53 Copynumber: 2.2 Consensus size: 53
43762093 AAAGTGTATA
* *
43762103 TTTTTAAAAGATTTAGTATTTATTAGTATAATGTGTAAAAAATTATATGAATT
1 TTTTTAAAAGATTTAATATTTATTAGTATAATATGTAAAAAATTATATGAATT
*
43762156 TTTTTAAAAGATTTAATATTTATTAGTATAATATGTAAAAATTTATATGAATT
1 TTTTTAAAAGATTTAATATTTATTAGTATAATATGTAAAAAATTATATGAATT
*
43762209 TATGTTAAAA
1 T-TTTTAAAA
43762219 AGATGGAAAG
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 51 0.88
54 7 0.12
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.47
Consensus pattern (53 bp):
TTTTTAAAAGATTTAATATTTATTAGTATAATATGTAAAAAATTATATGAATT
Found at i:43766263 original size:76 final size:76
Alignment explanation
Indices: 43766119--43766309 Score: 311
Period size: 76 Copynumber: 2.6 Consensus size: 76
43766109 CTCGAAGGTC
* * *
43766119 TTAGACATTTTC-TTTTGTCTATATCAATATAGA--TT-TT-ATTAATAAATAAACAACTCAACC
1 TTAGACGTTTTCTTTTTATCTATATTAATATAGATTTTATTAATTAATAAATAAACAACTCAACC
43766179 AGATGAAAGCT
66 AGATGAAAGCT
43766190 TTAGACGTTTTCTTTTTATCTATATTAATATAGATTTTATTAATTAATAAATAAACAACTCAACC
1 TTAGACGTTTTCTTTTTATCTATATTAATATAGATTTTATTAATTAATAAATAAACAACTCAACC
*
43766255 ATATGAAAGCT
66 AGATGAAAGCT
43766266 TTAGACGTTTTCTTTTTATCTATATTAATATAGATTTTATTAAT
1 TTAGACGTTTTCTTTTTATCTATATTAATATAGATTTTATTAAT
43766310 ATTGATGTCG
Statistics
Matches: 111, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
71 11 0.10
72 19 0.17
74 2 0.02
75 2 0.02
76 77 0.69
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (76 bp):
TTAGACGTTTTCTTTTTATCTATATTAATATAGATTTTATTAATTAATAAATAAACAACTCAACC
AGATGAAAGCT
Found at i:43766311 original size:21 final size:21
Alignment explanation
Indices: 43766279--43766340 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
43766269 GACGTTTTCT
43766279 TTTTATCT-ATATTAATATAGA
1 TTTTAT-TAATATTAATATAGA
* * *
43766300 TTTTATTAATATTGATGTCGA
1 TTTTATTAATATTAATATAGA
*
43766321 TTTT-TTATTA-TAATATAGA
1 TTTTATTAATATTAATATAGA
43766340 T
1 T
43766341 AAAAGAAAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 7 0.21
20 6 0.18
21 20 0.61
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (21 bp):
TTTTATTAATATTAATATAGA
Found at i:43767802 original size:15 final size:16
Alignment explanation
Indices: 43767772--43767810 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
43767762 TAGTAAAAAT
43767772 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
43767789 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
43767804 ATAATTT
1 ATAATTT
43767811 TTAGATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:43769711 original size:12 final size:14
Alignment explanation
Indices: 43769683--43769715 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
43769673 TTAAATTAGT
43769683 AATTAATAGATAAA
1 AATTAATAGATAAA
43769697 AATTAATA-A-AAA
1 AATTAATAGATAAA
43769709 AATTAAT
1 AATTAAT
43769716 TTATATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 1 0.05
14 8 0.42
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
AATTAATAGATAAA
Found at i:43788965 original size:22 final size:24
Alignment explanation
Indices: 43788911--43788965 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
43788901 GAGAAGGGTA
* *
43788911 AAAAAATAATTAAGAAAAATGCAG
1 AAAAAATAAATAAGAAAAATGAAG
43788935 AAAATAATAAATAA-AAAAA-GAAG
1 AAAA-AATAAATAAGAAAAATGAAG
*
43788958 GAAAAATA
1 AAAAAATA
43788966 GTCCCCACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 6 0.22
24 9 0.33
25 8 0.30
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.15
Consensus pattern (24 bp):
AAAAAATAAATAAGAAAAATGAAG
Found at i:43790503 original size:22 final size:22
Alignment explanation
Indices: 43790441--43790504 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
43790431 AAAAACAGAT
*
43790441 ATGATAAAAATTTATA-ATGAT
1 ATGATAAAAATTTATACATGAC
* *** *
43790462 ATTATTAAAAAAAAAAACATGAC
1 ATGA-TAAAAATTTATACATGAC
43790485 ATGATAAAAATTTATACATG
1 ATGATAAAAATTTATACATG
43790505 TTTTTATTAC
Statistics
Matches: 30, Mismatches: 11, Indels: 3
0.68 0.25 0.07
Matches are distributed among these distances:
21 3 0.10
22 20 0.67
23 7 0.23
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGATAAAAATTTATACATGAC
Found at i:43792715 original size:31 final size:33
Alignment explanation
Indices: 43792669--43792738 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
43792659 GTTCAAGGTA
*
43792669 AAAAAAGTTACCAAAA-TTATGTGTTAGATA-G
1 AAAAAAGTTACCAAAAGTTATGTATTAGATATG
43792700 TAAAAAAGTTA-CAAAAGTTATGTATTAGATATG
1 -AAAAAAGTTACCAAAAGTTATGTATTAGATATG
43792733 AAAAAA
1 AAAAAA
43792739 TTGCTGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
31 5 0.14
32 29 0.83
33 1 0.03
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (33 bp):
AAAAAAGTTACCAAAAGTTATGTATTAGATATG
Found at i:43793415 original size:30 final size:30
Alignment explanation
Indices: 43793334--43793416 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
43793324 TCATTATCCC
** *
43793334 TTTACTTTTTATAAATTCGAAAA-TTAGTTTT
1 TTTA-TTTTT-TAAATTTTAAAATTTAGTCTT
*
43793365 TTTA-TTTTT-ATTTTTAAAAATTTAGTCTT
1 TTTATTTTTTAAATTTT-AAAATTTAGTCTT
43793394 TTTATTTTTTAAATTTTAAAATT
1 TTTATTTTTTAAATTTTAAAATT
43793417 CAAGTCCAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.07
28 5 0.12
29 15 0.35
30 11 0.26
31 9 0.21
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (30 bp):
TTTATTTTTTAAATTTTAAAATTTAGTCTT
Found at i:43805473 original size:7 final size:7
Alignment explanation
Indices: 43805463--43805489 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
43805453 GTTTTGAGCC
43805463 AAAAAAT
1 AAAAAAT
43805470 AAAAAAT
1 AAAAAAT
43805477 AAAAAAT
1 AAAAAAT
43805484 AAAAAA
1 AAAAAA
43805490 AAATCGGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:43806459 original size:24 final size:24
Alignment explanation
Indices: 43806427--43806475 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
43806417 GGCAAGTGAA
43806427 TGCTTAACTATGTAATCTATTCAG
1 TGCTTAACTATGTAATCTATTCAG
43806451 TGCTTAACTATGTAATCTATTCAG
1 TGCTTAACTATGTAATCTATTCAG
43806475 T
1 T
43806476 CTAAACATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (24 bp):
TGCTTAACTATGTAATCTATTCAG
Found at i:43811389 original size:33 final size:32
Alignment explanation
Indices: 43811329--43811398 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
43811319 TATATTTTTT
* *
43811329 AAAATAAAATCTGTTTAAAATGCAAAAAACTTA
1 AAAATAAAATATGTTTAAAATACAAAAAA-TTA
* *
43811362 AAAATAAAATAT-TTTGAAAATATAAAAAATTC
1 AAAATAAAATATGTTT-AAAATACAAAAAATTA
43811394 AAAAT
1 AAAAT
43811399 TTAATGCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (32 bp):
AAAATAAAATATGTTTAAAATACAAAAAATTA
Found at i:43812924 original size:29 final size:29
Alignment explanation
Indices: 43812855--43812924 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
43812845 CTTTTCAATT
*
43812855 ATTTAATGAT-ATTTTAATAATTTTTTTC
1 ATTTAATGATAATTTTAATAATATTTTTC
* * *
43812883 ATGTCATTGATAATTTTGATAATATTTTTC
1 AT-TTAATGATAATTTTAATAATATTTTTC
43812913 -TTTAATAGATAA
1 ATTTAAT-GATAA
43812925 ATGAAAAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
28 5 0.15
29 12 0.36
30 16 0.48
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.54
Consensus pattern (29 bp):
ATTTAATGATAATTTTAATAATATTTTTC
Found at i:43816730 original size:6 final size:6
Alignment explanation
Indices: 43816719--43816802 Score: 50
Period size: 6 Copynumber: 14.3 Consensus size: 6
43816709 TAATTGAAAA
* * * **
43816719 TAAATT TAAATT TAAA-G TAAATT TAAACTC AAAAAA TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAA-TT TAAATT TAAATT TAAATT
* * *
43816767 TAAA-A TAAATT TAAACT T--ATT TAAAATT AAAATT TA
1 TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT TA
43816803 GGTAGAATTA
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
4 3 0.05
5 8 0.14
6 39 0.68
7 7 0.12
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (6 bp):
TAAATT
Found at i:43816730 original size:17 final size:17
Alignment explanation
Indices: 43816705--43816781 Score: 91
Period size: 17 Copynumber: 4.4 Consensus size: 17
43816695 TTTTAATTTT
* *
43816705 ATTTTAATTGAAAATAA
1 ATTTAAATTTAAAATAA
*
43816722 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
**
43816739 ATTTAAACTCAAAAAATAA
1 ATTTAAA-T-TTAAAATAA
43816758 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
43816775 ATTTAAA
1 ATTTAAA
43816782 CTTATTTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
17 35 0.70
18 2 0.04
19 13 0.26
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:43816760 original size:36 final size:36
Alignment explanation
Indices: 43816715--43816783 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
43816705 ATTTTAATTG
*
43816715 AAAATAAATTTAAATTTAAAGTAAATTTAAACTCAA
1 AAAATAAATTTAAATTTAAAATAAATTTAAACTCAA
43816751 AAAATAAATTTAAATTTAAAATAAATTTAAACT
1 AAAATAAATTTAAATTTAAAATAAATTTAAACT
43816784 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (36 bp):
AAAATAAATTTAAATTTAAAATAAATTTAAACTCAA
Found at i:43830234 original size:19 final size:20
Alignment explanation
Indices: 43830184--43830234 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
43830174 TTACAATAAC
*
43830184 TTTTTTAAAATAATTTTATA
1 TTTTTTAAAATAATATTATA
43830204 TTTTTATAAAAATTAATATT-TA
1 TTTTT-T-AAAA-TAATATTATA
43830226 -TTTTTAAAA
1 TTTTTTAAAA
43830235 AAAACATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 4 0.15
20 6 0.22
21 5 0.19
22 6 0.22
23 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTTTAAAATAATATTATA
Found at i:43831336 original size:29 final size:30
Alignment explanation
Indices: 43831303--43831359 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
43831293 TTGTTTAATA
43831303 TGTAA-TTGTATACATG-AACTTTGATTTTG
1 TGTAAGTT-TATACATGAAACTTTGATTTTG
*
43831332 TGTAAGTTTATACATGAAATTTTGATTT
1 TGTAAGTTTATACATGAAACTTTGATTT
43831360 AATTCAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (30 bp):
TGTAAGTTTATACATGAAACTTTGATTTTG
Found at i:43835004 original size:18 final size:18
Alignment explanation
Indices: 43834964--43835006 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
43834954 ATTCAAAGTG
43834964 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
43834982 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
43835000 TAATTAA
1 TAATTAA
43835007 AAATCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:43842548 original size:4 final size:4
Alignment explanation
Indices: 43842539--43842564 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
43842529 TTTCTTCACC
43842539 GTGG GTGG GTGG GTGG GTGG GTGG GT
1 GTGG GTGG GTGG GTGG GTGG GTGG GT
43842565 TCATCTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.73, T:0.27
Consensus pattern (4 bp):
GTGG
Found at i:43847812 original size:26 final size:27
Alignment explanation
Indices: 43847776--43847828 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
43847766 AAGTTTAAAG
43847776 TTTTACAAATAATTAAAAGATAAAATA
1 TTTTACAAATAATTAAAAGATAAAATA
* *
43847803 TTTTA-AAATAATTCAACGATAAAATA
1 TTTTACAAATAATTAAAAGATAAAATA
43847829 GGTTTACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.34
Consensus pattern (27 bp):
TTTTACAAATAATTAAAAGATAAAATA
Found at i:43848804 original size:29 final size:28
Alignment explanation
Indices: 43848772--43848828 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
43848762 TAAAAGTAAC
* * *
43848772 TTTTTTTAATTAATTATGTAAATAATTTA
1 TTTTTTT-ATTAAATACGAAAATAATTTA
43848801 TTTTTTTATTAAATACGAAAATAATTTA
1 TTTTTTTATTAAATACGAAAATAATTTA
43848829 AAATTTACAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (28 bp):
TTTTTTTATTAAATACGAAAATAATTTA
Found at i:43849308 original size:75 final size:78
Alignment explanation
Indices: 43849166--43849308 Score: 177
Period size: 75 Copynumber: 1.9 Consensus size: 78
43849156 ATCATTTATA
* * * * * *
43849166 TTTTTAAAATAAAGTTAAATATTTTTTTGGTGTTGTCATATTAAATGGCTCTACCATTTTCTCTA
1 TTTTTAAAATAAAGTTAAATATTTTTTTGGTGTTGCCATATTAAATGACGCCACCACTTCCTCTA
43849231 AATATTTTTATTT
66 AATATTTTTATTT
* *
43849244 TTTTTAAAA-AAATTTAAAT-TTTTTTTGGTG-TGCCATATTATATGACGCCACCACCTTCCT-T
1 TTTTTAAAATAAAGTTAAATATTTTTTTGGTGTTGCCATATTAAATGACGCCACCA-CTTCCTCT
43849305 AAAT
65 AAAT
43849309 GAATTTTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
75 23 0.41
76 15 0.27
77 9 0.16
78 9 0.16
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (78 bp):
TTTTTAAAATAAAGTTAAATATTTTTTTGGTGTTGCCATATTAAATGACGCCACCACTTCCTCTA
AATATTTTTATTT
Found at i:43849340 original size:11 final size:11
Alignment explanation
Indices: 43849324--43849357 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
43849314 TTTTAAAACG
43849324 ATTTATTATTT
1 ATTTATTATTT
43849335 ATTTATTACTTT
1 ATTTATTA-TTT
43849347 -TTTATTATTT
1 ATTTATTATTT
43849357 A
1 A
43849358 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.14
11 15 0.71
12 3 0.14
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTTATTATTT
Found at i:43849597 original size:99 final size:99
Alignment explanation
Indices: 43849490--43849711 Score: 381
Period size: 99 Copynumber: 2.2 Consensus size: 99
43849480 TGATGACGTT
*
43849490 ATTTAATATGGCACCATCAAAAAAATTTAAATTTCTAAAATATAAATATTAAATAATGAAAAAGG
1 ATTTAATATGGCACCATCAAAAAAATTTAAATTTCTAAAATATAAATATTAAATAATAAAAAAGG
*
43849555 AAAGACTGTTAGATTTTGGAAAAATAGTGACGCC
66 AAAGACTGTCAGATTTTGGAAAAATAGTGACGCC
43849589 ATTTAATATGGCACCATCAAAAAAATTTAAATTTCTAAAATATAAATATTAAATAATAAAAAAGG
1 ATTTAATATGGCACCATCAAAAAAATTTAAATTTCTAAAATATAAATATTAAATAATAAAAAAGG
* * * *
43849654 AAAGGCTGTCAGATTTTTGAAAAATGGTGACGTC
66 AAAGACTGTCAGATTTTGGAAAAATAGTGACGCC
*
43849688 ATTTAATATGGCCCCATCAAAAAA
1 ATTTAATATGGCACCATCAAAAAA
43849712 GGTAATATTG
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 116 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (99 bp):
ATTTAATATGGCACCATCAAAAAAATTTAAATTTCTAAAATATAAATATTAAATAATAAAAAAGG
AAAGACTGTCAGATTTTGGAAAAATAGTGACGCC
Found at i:43849894 original size:150 final size:149
Alignment explanation
Indices: 43849734--43850018 Score: 444
Period size: 150 Copynumber: 1.9 Consensus size: 149
43849724 TTCAAGTCCT
* * * * * * *
43849734 TTTATTTTTAATTTTTTTAGTATTTTCATGGTATTTATACAGGTGGCGCCATATTATATGGCTCC
1 TTTATTTTTAAATTTTTTAATATTTTCATGATATTTATACAAGTGACACCATATTATATGACTCC
* **
43849799 ACCAACTTTTACTGTAGATTTTAGGTTATTTTCGTATTTAATTAAAAAAATGGATTATTTACGTA
66 ACCAACTTTTACTGTAAATTTTAGGTTATTTTCGTATTTAATTAAAAAAATAAATTATTTACGTA
43849864 ATTAAATATTTCCATGGTA
131 ATTAAATATTTCCATGGTA
* *
43849883 TTTATTTTTTAAATTTTTTAATATTTTCATGATATTTATATAAGTGACACCATATTATATGACTT
1 TTTA-TTTTTAAATTTTTTAATATTTTCATGATATTTATACAAGTGACACCATATTATATGACTC
*
43849948 CACCAACTTTTACTGTAAATTTTAGGTTATTTTTGTATTTAATTAAAAAAATAAATTATTTACGT
65 CACCAACTTTTACTGTAAATTTTAGGTTATTTTCGTATTTAATTAAAAAAATAAATTATTTACGT
43850013 AATTAA
130 AATTAA
43850019 TTAAAAAAAG
Statistics
Matches: 122, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
149 4 0.03
150 118 0.97
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.48
Consensus pattern (149 bp):
TTTATTTTTAAATTTTTTAATATTTTCATGATATTTATACAAGTGACACCATATTATATGACTCC
ACCAACTTTTACTGTAAATTTTAGGTTATTTTCGTATTTAATTAAAAAAATAAATTATTTACGTA
ATTAAATATTTCCATGGTA
Found at i:43851644 original size:165 final size:163
Alignment explanation
Indices: 43851180--43851774 Score: 639
Period size: 165 Copynumber: 3.6 Consensus size: 163
43851170 TTTTAAATCC
* *
43851180 AAATTACAAAATTCACCGCCGTTTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCG
1 AAATTACAAAATTCATCGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCG
* * * * *
43851245 CTCTACCAGCTGAGCTAAGACGGCTGCTGATGTAA-AGTAGTATTGT-GATGAATCACCAGTATT
66 CTCTACCAGCTGAGCTAAGACGGCTACTGATG-AATTG-AGAATAGTGGATG-ATCATCAGTATT
* * *
43851308 CTTCCTCGTCTCTTCGAGGT-GGTAAACAAAATGTAAAAATAG
128 -TT--T--TCTCTTCTA-TTCGGTAAAAAAAATGT-AAAATAG
* * *
43851350 ATATTTCAAAGTT-ATTCGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGC
1 AAATTACAAAATTCA-TCGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGC
* * * * *
43851414 GCTCTACCGGCTGAGCTAAAACGGCTACTCAT-ATACTATG-GAATAGT-GACGGATCATCGGTA
65 GCTCTACCAGCTGAGCTAAGACGGCTACTGATGA-A-T-TGAGAATAGTGGA-TGATCATCAGTA
* * *
43851476 TTTTTTTTCTTCTATTCGGTAAAGAAAAAAGTAAAAGAG
126 TTTTTTCTCTTCTATTCGGTAAA-AAAAATGTAAAATAG
* * *
43851515 AAATTACAAAACTCATCGCCGACTGTGGGAATCGAACCCACGACCACGTGTTTAAAAGCCACGCG
1 AAATTACAAAATTCATCGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCG
* * * * *
43851580 CTCTACCGGCTGAGCTAAGACGGCTACGGATGAATTGCAGCATAGTGGTTGATCATCTGTATTTT
66 CTCTACCAGCTGAGCTAAGACGGCTACTGATGAATTG-AGAATAGTGGATGATCATCAGTATTTT
* * * * * * *
43851645 CTCTCGTCTCTTCGGT-AAACAACTGTCAAATAA
130 TTCTCTTCTATTCGGTAAAAAAAATGTAAAATAG
* *
43851678 AAATTGCAAAATTCAACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCG
1 AAATTACAAAATTCATCGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCG
43851743 CTCTACCAGCTGAGCTAAGACGGCTACTGATG
66 CTCTACCAGCTGAGCTAAGACGGCTACTGATG
43851775 GCTCAATATC
Statistics
Matches: 361, Mismatches: 51, Indels: 33
0.81 0.11 0.07
Matches are distributed among these distances:
163 101 0.28
164 4 0.01
165 137 0.38
166 9 0.02
167 1 0.00
168 1 0.00
169 4 0.01
170 102 0.28
171 1 0.00
172 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (163 bp):
AAATTACAAAATTCATCGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCG
CTCTACCAGCTGAGCTAAGACGGCTACTGATGAATTGAGAATAGTGGATGATCATCAGTATTTTT
TCTCTTCTATTCGGTAAAAAAAATGTAAAATAG
Found at i:43862173 original size:2 final size:2
Alignment explanation
Indices: 43862166--43862192 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43862156 GCTTTTCTGG
43862166 TA 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 TA T
43862193 GTTGGTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43862994 original size:61 final size:61
Alignment explanation
Indices: 43862899--43863018 Score: 231
Period size: 61 Copynumber: 2.0 Consensus size: 61
43862889 GCAGCTATAA
*
43862899 GGAAATCCCATGTTGACCTGATGATCAGGGTATTCACTGTTCCAGATGTGATCTGGATTCG
1 GGAAATCCCATGTTGACCTGATGATCAGGGTATTCACCGTTCCAGATGTGATCTGGATTCG
43862960 GGAAATCCCATGTTGACCTGATGATCAGGGTATTCACCGTTCCAGATGTGATCTGGATT
1 GGAAATCCCATGTTGACCTGATGATCAGGGTATTCACCGTTCCAGATGTGATCTGGATT
43863019 TGAATCCCGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (61 bp):
GGAAATCCCATGTTGACCTGATGATCAGGGTATTCACCGTTCCAGATGTGATCTGGATTCG
Found at i:43867277 original size:3 final size:3
Alignment explanation
Indices: 43867269--43867297 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
43867259 GGATTCCTTA
43867269 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
43867298 AGTTCCTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:43871537 original size:90 final size:90
Alignment explanation
Indices: 43871384--43871656 Score: 483
Period size: 90 Copynumber: 3.0 Consensus size: 90
43871374 TCTCCAGGTC
* *
43871384 TTTGGCTGCTATTCCCCTTGCTGAATGACGTAGACTTCACATTTATCTCCTTTGAGTTCATAGCT
1 TTTGGCTGCTATTCCCCTTGCTGAATGATGTAGACTTCACATTTATCTCCTTTGAGATCATAGCT
43871449 GAGCCCTCTTTCCTGGTGACCTGTT
66 GAGCCCTCTTTCCTGGTGACCTGTT
*
43871474 TTTGGCTGCTATTCCCCTTGCTGGATGATGTAGACTTCACATTTATCTCCTTTGAGATCATAGCT
1 TTTGGCTGCTATTCCCCTTGCTGAATGATGTAGACTTCACATTTATCTCCTTTGAGATCATAGCT
43871539 GAGCCCTCTTTCCTGGTGACCTGTT
66 GAGCCCTCTTTCCTGGTGACCTGTT
* **
43871564 TTTGGCTGCTATTCTCCTTGCTGAATGATGTAGACTTCACATCCATCTCCTTTGAGATCATAGCT
1 TTTGGCTGCTATTCCCCTTGCTGAATGATGTAGACTTCACATTTATCTCCTTTGAGATCATAGCT
*
43871629 GAGCCCTCTATCCTGGTGACCTGTT
66 GAGCCCTCTTTCCTGGTGACCTGTT
43871654 TTT
1 TTT
43871657 TATCCCTAAA
Statistics
Matches: 175, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 175 1.00
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (90 bp):
TTTGGCTGCTATTCCCCTTGCTGAATGATGTAGACTTCACATTTATCTCCTTTGAGATCATAGCT
GAGCCCTCTTTCCTGGTGACCTGTT
Found at i:43886802 original size:20 final size:20
Alignment explanation
Indices: 43886777--43886816 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43886767 CAAGTTGAGG
*
43886777 TTTGCAAACTAGCTTTGGGT
1 TTTGCAAACTAACTTTGGGT
*
43886797 TTTGCATACTAACTTTGGGT
1 TTTGCAAACTAACTTTGGGT
43886817 CTGCAGTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (20 bp):
TTTGCAAACTAACTTTGGGT
Found at i:43902801 original size:16 final size:17
Alignment explanation
Indices: 43902780--43902813 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
43902770 ATTGATGGAG
43902780 TCAAAAAAAATTA-ATA
1 TCAAAAAAAATTATATA
*
43902796 TCAAAATAAATTATATA
1 TCAAAAAAAATTATATA
43902813 T
1 T
43902814 TTTTATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
TCAAAAAAAATTATATA
Found at i:43904132 original size:23 final size:25
Alignment explanation
Indices: 43904098--43904148 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 25
43904088 TTTACAAAAT
*
43904098 ATAAATCTTAATAT-T-TCAATATA
1 ATAAATCTTAATATATATAAATATA
43904121 ATAATATC-TAATATATATAAATATA
1 ATAA-ATCTTAATATATATAAATATA
43904146 ATA
1 ATA
43904149 CAAATTATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 10 0.42
24 4 0.17
25 10 0.42
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAAATCTTAATATATATAAATATA
Found at i:43908928 original size:6 final size:6
Alignment explanation
Indices: 43908917--43908943 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43908907 TGCATGCATG
43908917 CATGGA CATGGA CATGGA CATGGA CAT
1 CATGGA CATGGA CATGGA CATGGA CAT
43908944 ACCATTGGCC
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:0.33, C:0.19, G:0.30, T:0.19
Consensus pattern (6 bp):
CATGGA
Found at i:43929941 original size:17 final size:17
Alignment explanation
Indices: 43929901--43929941 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
43929891 AATTAAGTTG
*
43929901 TAATTTTTTTATATAAT
1 TAATTATTTTATATAAT
43929918 TAA-TATTTTA-ATAATT
1 TAATTATTTTATATAA-T
43929934 TAATTATT
1 TAATTATT
43929942 GAATTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTATTTTATATAAT
Found at i:43954800 original size:24 final size:24
Alignment explanation
Indices: 43954771--43954819 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
43954761 AATAGAGTTT
*
43954771 AGTTTAATTGAAATAAATAAACAG
1 AGTTTAATTGAAACAAATAAACAG
43954795 AGTTTAATTGAAACAAATAAACAG
1 AGTTTAATTGAAACAAATAAACAG
43954819 A
1 A
43954820 ATTTGGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (24 bp):
AGTTTAATTGAAACAAATAAACAG
Found at i:43955159 original size:12 final size:13
Alignment explanation
Indices: 43955142--43955177 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
43955132 TTATGAAATG
43955142 ATGAATAATTTT-
1 ATGAATAATTTTA
43955154 ATGAATAATTTTA
1 ATGAATAATTTTA
43955167 AGTGAATAATT
1 A-TGAATAATT
43955178 GAAAGTAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
13 1 0.05
14 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (13 bp):
ATGAATAATTTTA
Found at i:43959661 original size:28 final size:28
Alignment explanation
Indices: 43959629--43959691 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
43959619 TTGTACCAAC
43959629 AACACAAAACCATGTTCCATACGTGAAA
1 AACACAAAACCATGTTCCATACGTGAAA
43959657 AACACAAAACCATGTTCCATACGTGAAA
1 AACACAAAACCATGTTCCATACGTGAAA
43959685 AACACAA
1 AACACAA
43959692 CTTTTACCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.49, C:0.25, G:0.10, T:0.16
Consensus pattern (28 bp):
AACACAAAACCATGTTCCATACGTGAAA
Found at i:43968851 original size:2 final size:2
Alignment explanation
Indices: 43968846--43968875 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
43968836 TATGGAAAAC
*
43968846 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43968876 GAAATTAATT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:43975459 original size:32 final size:30
Alignment explanation
Indices: 43975402--43975460 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
43975392 TTTATCCCCT
*
43975402 AAAAATAATAAAAATTTGATTTAATTTTTA
1 AAAAATAATAAAAATTTAATTTAATTTTTA
*
43975432 AAAAATATTTAAAAATTATAATTTAATTT
1 AAAAATA-ATAAAAATT-TAATTTAATTT
43975461 CAATTCCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
31 8 0.32
32 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
AAAAATAATAAAAATTTAATTTAATTTTTA
Found at i:43987292 original size:2 final size:2
Alignment explanation
Indices: 43987285--43987311 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43987275 CAAGTACGGA
43987285 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
43987312 ATGCATGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:44004320 original size:11 final size:11
Alignment explanation
Indices: 44004270--44004341 Score: 55
Period size: 11 Copynumber: 6.9 Consensus size: 11
44004260 AATATCTCTA
*
44004270 AAATAATAATA
1 AAATAATAATT
*
44004281 ATAATAATAATA
1 A-AATAATAATT
*
44004293 AAATAAAAATT
1 AAATAATAATT
* *
44004304 ATATAATATTT
1 AAATAATAATT
44004315 AAATAATAA--
1 AAATAATAATT
44004324 AAATAA-AA-T
1 AAATAATAATT
44004333 -AATAATAAT
1 AAATAATAAT
44004342 AAACTAACGA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
8 7 0.14
9 8 0.16
11 24 0.48
12 11 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATAATT
Found at i:44004344 original size:14 final size:14
Alignment explanation
Indices: 44004268--44004344 Score: 84
Period size: 14 Copynumber: 5.3 Consensus size: 14
44004258 TAAATATCTC
44004268 TAAAATAATAATAA
1 TAAAATAATAATAA
44004282 TAATAATAATAA-AA
1 TAA-AATAATAATAA
*
44004296 TAAAAATTATATAATAT
1 T-AAAA-TA-ATAATAA
* *
44004313 TTAAATAATAAAAA
1 TAAAATAATAATAA
44004327 TAAAATAATAATAA
1 TAAAATAATAATAA
44004341 TAAA
1 TAAA
44004345 CTAACGAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 29 0.56
15 14 0.27
16 7 0.13
17 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAATAATAATAA
Found at i:44004355 original size:36 final size:36
Alignment explanation
Indices: 44004280--44004358 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 36
44004270 AAATAATAAT
* * ***
44004280 AATAATAATAATAAAATAAAAATTATATAATATTTA
1 AATAATAAAAATAAAATAAAAATAATATAATAACGA
*
44004316 AATAATAAAAATAAAATAATAATAATA-AACTAACGA
1 AATAATAAAAATAAAATAAAAATAATATAA-TAACGA
44004352 AATAATA
1 AATAATA
44004359 GCAAAAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 2 0.06
36 34 0.94
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (36 bp):
AATAATAAAAATAAAATAAAAATAATATAATAACGA
Found at i:44004358 original size:3 final size:3
Alignment explanation
Indices: 44004271--44004343 Score: 73
Period size: 3 Copynumber: 25.7 Consensus size: 3
44004261 ATATCTCTAA
* * * *
44004271 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAA AAT TAT -AT AAT ATT TA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
44004316 AAT AAT AAA AAT AA- AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
44004344 ACTAACGAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
2 7 0.12
3 50 0.88
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:44004584 original size:5 final size:5
Alignment explanation
Indices: 44004574--44004602 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
44004564 CATCTCAATT
44004574 TTTTA TTTTA -TTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
44004603 ATAATCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:44004589 original size:9 final size:10
Alignment explanation
Indices: 44004574--44004602 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
44004564 CATCTCAATT
44004574 TTTTATTTTA
1 TTTTATTTTA
44004584 -TTTATTTTA
1 TTTTATTTTA
44004593 TTTTATTTTA
1 TTTTATTTTA
44004603 ATAATCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:44004591 original size:14 final size:14
Alignment explanation
Indices: 44004574--44004600 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44004564 CATCTCAATT
44004574 TTTTATTTTATTTA
1 TTTTATTTTATTTA
44004588 TTTTATTTTATTT
1 TTTTATTTTATTT
44004601 TAATAATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTTATTTA
Found at i:44023681 original size:13 final size:13
Alignment explanation
Indices: 44023663--44023687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44023653 CATTTTTGTA
44023663 ATTATTATTTTAT
1 ATTATTATTTTAT
44023676 ATTATTATTTTA
1 ATTATTATTTTA
44023688 AAAATACCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATTATTTTAT
Found at i:44028441 original size:42 final size:42
Alignment explanation
Indices: 44028382--44028465 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
44028372 CAAATATTTT
*
44028382 TAAACTCAAATATAATTTCATTCTTCAAA-AACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCTT-AAATAACACTCATAAAC
* * *
44028424 TAAACCCAAATATAATTTTATTCTTAAATAATATTCATAAAC
1 TAAACCCAAATATAATTTCATTCTTAAATAACACTCATAAAC
44028466 AACTCTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 3 0.08
42 34 0.92
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.35
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCTTAAATAACACTCATAAAC
Found at i:44034785 original size:5 final size:5
Alignment explanation
Indices: 44034777--44034805 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
44034767 GAAGAGTAGA
44034777 GCAGT GCAGT GCAGT GCAGT GCAGT GCAG
1 GCAGT GCAGT GCAGT GCAGT GCAGT GCAG
44034806 AGTGATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.41, T:0.17
Consensus pattern (5 bp):
GCAGT
Found at i:44036259 original size:19 final size:22
Alignment explanation
Indices: 44036237--44036305 Score: 65
Period size: 27 Copynumber: 3.1 Consensus size: 22
44036227 TAATGCCACT
44036237 TTGGTTTTAT-T-C-ACAAAAG
1 TTGGTTTTATGTACTACAAAAG
44036256 TTGG-TTTATGTACTACAAAAG
1 TTGGTTTTATGTACTACAAAAG
44036277 TTGTGTTTGATTTATGTACTACAAAAG
1 TTG-G--T--TTTATGTACTACAAAAG
44036304 TT
1 TT
44036306 CACATCAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
18 5 0.12
19 5 0.12
20 1 0.02
21 10 0.24
22 1 0.02
27 19 0.46
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (22 bp):
TTGGTTTTATGTACTACAAAAG
Found at i:44037014 original size:3 final size:3
Alignment explanation
Indices: 44037008--44037039 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
44036998 AACGAAACAT
*
44037008 AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
44037040 AGAACTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:44042968 original size:5 final size:5
Alignment explanation
Indices: 44042960--44042996 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
44042950 TAATTAAATT
44042960 ATTTA ATTTA ATTTA ATTTA ATTT- ATATT- ATTTA ATT
1 ATTTA ATTTA ATTTA ATTTA ATTTA AT-TTA ATTTA ATT
44042997 ATATTGTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTA
Found at i:44042980 original size:15 final size:14
Alignment explanation
Indices: 44042944--44043001 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 14
44042934 AATCCGGGAA
* *
44042944 ATTAGTTAA-TTAA
1 ATTATTTAATTTAT
44042957 ATTATTTAATTTA-
1 ATTATTTAATTTAT
44042970 ATTTAATTTAATTTAT
1 A-TT-ATTTAATTTAT
44042986 ATTATTTAA-TTAT
1 ATTATTTAATTTAT
44042999 ATT
1 ATT
44043002 GTACACTTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
13 16 0.40
14 11 0.28
15 12 0.30
16 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
ATTATTTAATTTAT
Found at i:44043936 original size:24 final size:24
Alignment explanation
Indices: 44043897--44043948 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
44043887 TCAAATGCAT
44043897 CCTCCACCCCCAATGTATCAC-CCA
1 CCTCCACCCCCAATGTATC-CTCCA
* *
44043921 CCTCCACCGCCGATGTATCCTCCA
1 CCTCCACCCCCAATGTATCCTCCA
44043945 CCTC
1 CCTC
44043949 AAATGTATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.19, C:0.54, G:0.08, T:0.19
Consensus pattern (24 bp):
CCTCCACCCCCAATGTATCCTCCA
Found at i:44043944 original size:18 final size:18
Alignment explanation
Indices: 44043921--44043962 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
44043911 GTATCACCCA
**
44043921 CCTCCACCGCCGATGTAT
1 CCTCCACCGCAAATGTAT
*
44043939 CCTCCACCTCAAATGTAT
1 CCTCCACCGCAAATGTAT
44043957 CCTCCA
1 CCTCCA
44043963 TATCAGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.45, G:0.10, T:0.24
Consensus pattern (18 bp):
CCTCCACCGCAAATGTAT
Found at i:44047940 original size:7 final size:7
Alignment explanation
Indices: 44047930--44047956 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
44047920 AGAGTTTAGA
44047930 TTTAAGG
1 TTTAAGG
44047937 TTTAAGG
1 TTTAAGG
44047944 TTTAAGG
1 TTTAAGG
44047951 TTTAAG
1 TTTAAG
44047957 ATTTTGGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (7 bp):
TTTAAGG
Found at i:44048066 original size:28 final size:29
Alignment explanation
Indices: 44048006--44048066 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
44047996 AAAGTTCGAG
*
44048006 ATAAAAAAAATTACTAATGTATCAATAAC
1 ATAAAAAAAATTACTAATATATCAATAAC
*
44048035 ATAAAAAAAATTACTGAA-ATATCATTAA-
1 ATAAAAAAAATTACT-AATATATCAATAAC
44048063 ATAA
1 ATAA
44048067 TTTATCAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 23 0.79
30 2 0.07
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.28
Consensus pattern (29 bp):
ATAAAAAAAATTACTAATATATCAATAAC
Found at i:44051513 original size:6 final size:6
Alignment explanation
Indices: 44051496--44051526 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
44051486 AATACTAGTC
*
44051496 CTTCAG CATCAG CTTCAG CTTCAG CTTCAG C
1 CTTCAG CTTCAG CTTCAG CTTCAG CTTCAG C
44051527 ACATCAAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.35, G:0.16, T:0.29
Consensus pattern (6 bp):
CTTCAG
Found at i:44053662 original size:51 final size:51
Alignment explanation
Indices: 44053589--44053693 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
44053579 ATAATACAAT
44053589 TATTATAAAAGGGATAAATCTCTAATAACTTTGAACAAATGTATATTGTTA
1 TATTATAAAAGGGATAAATCTCTAATAACTTTGAACAAATGTATATTGTTA
44053640 TATTATAAAAGGGATAAATCTCTAATAACTTTGAACAAATGTATATTGTTA
1 TATTATAAAAGGGATAAATCTCTAATAACTTTGAACAAATGTATATTGTTA
44053691 TAT
1 TAT
44053694 ACGAATTTTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (51 bp):
TATTATAAAAGGGATAAATCTCTAATAACTTTGAACAAATGTATATTGTTA
Found at i:44057703 original size:8 final size:9
Alignment explanation
Indices: 44057680--44057708 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
44057670 TAAACGTGGT
44057680 GTAAAAATA
1 GTAAAAATA
44057689 GTAAAAATA
1 GTAAAAATA
44057698 GTAAAAATA
1 GTAAAAATA
44057707 GT
1 GT
44057709 GAAATCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (9 bp):
GTAAAAATA
Found at i:44060882 original size:29 final size:28
Alignment explanation
Indices: 44060827--44060910 Score: 71
Period size: 29 Copynumber: 2.8 Consensus size: 28
44060817 AAAATTTTAA
*
44060827 AATTTAAAAAGTAAAAGGATTGAAATTAACT
1 AATTTAAAAA-TAAAA-CATT-AAATTAACT
*
44060858 AATTTAAAAATATAAACATTAAATTTAATT
1 AATTTAAAAATA-AAACATTAAA-TTAACT
* *
44060888 AAATT-AAAATACAAATATTAAAT
1 AATTTAAAAATA-AAACATTAAAT
44060911 CCGCAACAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 1 0.02
29 18 0.39
30 14 0.30
31 13 0.28
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (28 bp):
AATTTAAAAATAAAACATTAAATTAACT
Found at i:44061581 original size:27 final size:29
Alignment explanation
Indices: 44061523--44061577 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 29
44061513 TTTGATGTAT
*
44061523 TTTTTTTCTTTTTATTTCCAAAAATTTAA
1 TTTTTTTCTATTTATTTCCAAAAATTTAA
*
44061552 TTTTTTT-TATTT-TTT-CAAAATTTTAA
1 TTTTTTTCTATTTATTTCCAAAAATTTAA
44061578 ATTTAGATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.42
27 3 0.12
28 4 0.17
29 7 0.29
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTTTTCTATTTATTTCCAAAAATTTAA
Found at i:44062018 original size:15 final size:16
Alignment explanation
Indices: 44061988--44062019 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
44061978 ATATGACAAC
44061988 TTTTTAAAATTATAAT
1 TTTTTAAAATTATAAT
44062004 TTTTTAAAATT-TAAT
1 TTTTTAAAATTATAAT
44062019 T
1 T
44062020 GTGTACTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTAAAATTATAAT
Found at i:44062450 original size:19 final size:20
Alignment explanation
Indices: 44062406--44062453 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
44062396 TTTATTTTCT
* *
44062406 TGTT-CTATTCTCATTGTTT
1 TGTTGCTATTCTCATTATTA
*
44062425 TGATGCTATT-TCATTATTA
1 TGTTGCTATTCTCATTATTA
44062444 TGTTGCTATT
1 TGTTGCTATT
44062454 ATTTTGTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.58
Consensus pattern (20 bp):
TGTTGCTATTCTCATTATTA
Found at i:44084172 original size:7 final size:7
Alignment explanation
Indices: 44084162--44084189 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
44084152 TATATTTTAT
44084162 ATATTAA
1 ATATTAA
44084169 ATATTAA
1 ATATTAA
44084176 ATATTAA
1 ATATTAA
44084183 ATATTAA
1 ATATTAA
44084190 TAACAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATTAA
Found at i:44087334 original size:26 final size:26
Alignment explanation
Indices: 44087298--44087355 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
44087288 CTTAAGATTA
44087298 TGCATACTTGTTTCAGTAGAACCTAT
1 TGCATACTTGTTTCAGTAGAACCTAT
*
44087324 TGCATACTTGTTTCAGTATAACCTAT
1 TGCATACTTGTTTCAGTAGAACCTAT
44087350 TGCATA
1 TGCATA
44087356 TTTCGGTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (26 bp):
TGCATACTTGTTTCAGTAGAACCTAT
Found at i:44091130 original size:21 final size:22
Alignment explanation
Indices: 44091089--44091130 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
44091079 TAAATATTAG
*
44091089 ATTAAATTTAATATTAAATTTT
1 ATTAAATTTAATATGAAATTTT
44091111 ATTAAA-TTAATA-GAATATTT
1 ATTAAATTTAATATGAA-ATTT
44091131 ACCCACAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 10 0.56
22 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAAATTTAATATGAAATTTT
Found at i:44091179 original size:12 final size:12
Alignment explanation
Indices: 44091150--44091182 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
44091140 ATAGACATTA
*
44091150 AATTAATAAAAT
1 AATTATTAAAAT
44091162 -ATTATTAAAAT
1 AATTATTAAAAT
44091173 AATTATTAAA
1 AATTATTAAA
44091183 TTAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATTATTAAAAT
Found at i:44092062 original size:23 final size:23
Alignment explanation
Indices: 44092028--44092081 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
44092018 AGATAATGAA
*
44092028 TTTAGGGGTAAT-AGACATTCATTC
1 TTTA-GGGTAATGA-ACAATCATTC
44092052 TTTAGGGTAATGAACAATCATTC
1 TTTAGGGTAATGAACAATCATTC
44092075 TTTAGGG
1 TTTAGGG
44092082 GTTATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (23 bp):
TTTAGGGTAATGAACAATCATTC
Found at i:44092230 original size:33 final size:29
Alignment explanation
Indices: 44092170--44092225 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
44092160 TTATACAATT
*
44092170 GATAAGATAGTCTTCAAAATAGTTAAAAG
1 GATAAGATAGTCTTCAAAATAATTAAAAG
* *
44092199 GATAATATAGTCTTCAAAATAAATAAA
1 GATAAGATAGTCTTCAAAATAATTAAA
44092226 TAAAACAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (29 bp):
GATAAGATAGTCTTCAAAATAATTAAAAG
Found at i:44093337 original size:84 final size:83
Alignment explanation
Indices: 44093203--44093412 Score: 230
Period size: 84 Copynumber: 2.5 Consensus size: 83
44093193 AGAGAATGAA
* * *
44093203 AATCAAATATGGGAAAGGAAATA-ATAACA-ACAATGTAAAATAGAGATATGAAA-GAGAATTGA
1 AATCAAATATGAGAAAGGAAATAGATAACATA-TATGAAAAATAGAGATATGAAAGGA-AATTGA
*
44093265 ATATTTTATTG-AAAATAAAT
64 ATATTTTA-TGAAAAATAAAG
* *
44093285 TATCAAATATGAGAAAGGAAATAGTATAACATATATGAAAAATAGAGATATGAAAGGAAATTTAA
1 AATCAAATATGAGAAAGGAAATAG-ATAACATATATGAAAAATAGAGATATGAAAGGAAATTGAA
*
44093350 TATTTTATGAAAAATAGAG
65 TATTTTATGAAAAATAAAG
* ** * * *
44093369 AACCAAATACAAGAAAAGAAAGAGAATAACATATATGGAAAATA
1 AATCAAATATGAGAAAGGAAATAG-ATAACATATATGAAAAATA
44093413 AAAAATCAAA
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
82 21 0.19
83 2 0.02
84 82 0.76
85 3 0.03
ACGTcount: A:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (83 bp):
AATCAAATATGAGAAAGGAAATAGATAACATATATGAAAAATAGAGATATGAAAGGAAATTGAAT
ATTTTATGAAAAATAAAG
Found at i:44093341 original size:39 final size:37
Alignment explanation
Indices: 44093297--44093369 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
44093287 TCAAATATGA
44093297 GAAAGGAAATAGTATAACA-TATATGAAAAATAGAGATAT
1 GAAAGGAAAT--T-TAACATTATATGAAAAATAGAGATAT
* *
44093336 GAAAGGAAATTTAATATTTTATGAAAAATAGAGA
1 GAAAGGAAATTTAACATTATATGAAAAATAGAGA
44093370 ACCAAATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 4 0.13
37 17 0.55
39 10 0.32
ACGTcount: A:0.55, C:0.01, G:0.18, T:0.26
Consensus pattern (37 bp):
GAAAGGAAATTTAACATTATATGAAAAATAGAGATAT
Found at i:44093452 original size:21 final size:21
Alignment explanation
Indices: 44093387--44093452 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
44093377 ACAAGAAAAG
* *
44093387 AAAGAGAATAACATATATGGA
1 AAAGAGAATAATAAATATGGA
* * ***
44093408 AAATA-AAAAATCAAATACAAA
1 AAAGAGAATAAT-AAATATGGA
44093429 AAAGAGAATAATAAATATGGA
1 AAAGAGAATAATAAATATGGA
44093450 AAA
1 AAA
44093453 TTTATTTTCC
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
20 4 0.13
21 22 0.71
22 5 0.16
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.17
Consensus pattern (21 bp):
AAAGAGAATAATAAATATGGA
Found at i:44099962 original size:6 final size:6
Alignment explanation
Indices: 44099951--44099987 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
44099941 TATTTTGGCC
*
44099951 AATTAA AATTAA AATTAA AATTAA AGTTAA AATTAA A
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA A
44099988 GTCATCAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (6 bp):
AATTAA
Found at i:44104089 original size:15 final size:15
Alignment explanation
Indices: 44104066--44104101 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
44104056 AATTTATAAA
* *
44104066 TTTTAATTTAATTAT
1 TTTTTATTTAAATAT
44104081 TTTTTATTTAAATAT
1 TTTTTATTTAAATAT
44104096 TTTTTA
1 TTTTTA
44104102 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTATTTAAATAT
Found at i:44104417 original size:29 final size:31
Alignment explanation
Indices: 44104385--44104450 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
44104375 TAAGGATTGA
* * *
44104385 ATCAAATTT-ATCTTTATATTATCAAATAG-
1 ATCAAATTTAATCTCTATACTATCAAAAAGT
*
44104414 ATC-AATTTAATCTCTATACTATTAAAAAGT
1 ATCAAATTTAATCTCTATACTATCAAAAAGT
44104444 ATCAAAT
1 ATCAAAT
44104451 AAGTCTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 5 0.17
29 19 0.63
30 3 0.10
31 3 0.10
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (31 bp):
ATCAAATTTAATCTCTATACTATCAAAAAGT
Found at i:44104795 original size:3 final size:3
Alignment explanation
Indices: 44104770--44104813 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
44104760 AAGTTTGTCA
* * *
44104770 ACC ATC ACC ATC ACC ATC ACC ACC ACC ACC ACC ACC ACC ACC AC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC AC
44104814 GACAACAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.59, G:0.00, T:0.07
Consensus pattern (3 bp):
ACC
Found at i:44108081 original size:2 final size:2
Alignment explanation
Indices: 44108074--44108149 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
44108064 CGATAAATTG
44108074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44108116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44108150 TCAATTGTTG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44111122 original size:4 final size:4
Alignment explanation
Indices: 44111096--44111157 Score: 88
Period size: 4 Copynumber: 15.5 Consensus size: 4
44111086 CCAGCCTACG
* * * *
44111096 ATGT ATAT ATAT ATAT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44111144 ATGT ATGT ATGT AT
1 ATGT ATGT ATGT AT
44111158 AGGTGTATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:44112955 original size:65 final size:65
Alignment explanation
Indices: 44112851--44112981 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
44112841 AGAATTCATC
*
44112851 TGGTGGTCCTTTGTATCTATACTTGTGATTGGTCAAAGCTATGGGTTCCACATGTTAGTCTCTCT
1 TGGTGGTCCTTTGTATCTATACTTATGATTGGTCAAAGCTATGGGTTCCACATGTTAGTCTCTCT
44112916 TGGTGGTCCTTTGTATCTATACTTATGATTGGTCAAAGCTATGGGTTCCACATGTTAGTCTCTCT
1 TGGTGGTCCTTTGTATCTATACTTATGATTGGTCAAAGCTATGGGTTCCACATGTTAGTCTCTCT
44112981 T
1 T
44112982 TTGTTTGAAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (65 bp):
TGGTGGTCCTTTGTATCTATACTTATGATTGGTCAAAGCTATGGGTTCCACATGTTAGTCTCTCT
Found at i:44118010 original size:25 final size:25
Alignment explanation
Indices: 44117957--44118014 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
44117947 TAATGTTTAC
*
44117957 ATTTTTT-ATTAATTTGATATTTATT
1 ATTTTTTAATTAATTTGATATTCA-T
*
44117982 ATTTTTTAATTAAATTTGATCTTCA-
1 ATTTTTTAATT-AATTTGATATTCAT
44118007 ATTTTTTA
1 ATTTTTTA
44118015 GTAAATATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 15 0.52
26 3 0.10
27 11 0.38
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (25 bp):
ATTTTTTAATTAATTTGATATTCAT
Found at i:44118012 original size:26 final size:25
Alignment explanation
Indices: 44117957--44118013 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
44117947 TAATGTTTAC
* *
44117957 ATTTTTTATTAATTTGATATTTATT
1 ATTTTTTATTAATTTGATATTCAAT
*
44117982 ATTTTTTAATTAAATTTGATCTTCAAT
1 ATTTTTT-ATT-AATTTGATATTCAAT
44118009 -TTTTT
1 ATTTTT
44118014 AGTAAATATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 7 0.26
26 8 0.30
27 12 0.44
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (25 bp):
ATTTTTTATTAATTTGATATTCAAT
Found at i:44122599 original size:17 final size:17
Alignment explanation
Indices: 44122568--44122601 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44122558 CATTTTGGCT
**
44122568 TTTTAAATTTTTAAAAA
1 TTTTAAATTAATAAAAA
44122585 TTTTAAATTAATAAAAA
1 TTTTAAATTAATAAAAA
44122602 AATTGCAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTTAAATTAATAAAAA
Found at i:44128192 original size:30 final size:30
Alignment explanation
Indices: 44128158--44128300 Score: 191
Period size: 30 Copynumber: 4.8 Consensus size: 30
44128148 TAAAGTAAGC
44128158 TTAGGGGTCAAAATATAATTTTTGAAAAGT
1 TTAGGGGTCAAAATATAATTTTTGAAAAGT
* **
44128188 TTAGGAGTCAAAATATAATTTTCAAAAAGT
1 TTAGGGGTCAAAATATAATTTTTGAAAAGT
44128218 TTAGGGGTCAAAATATAATTTTT-AGAAAGT
1 TTAGGGGTCAAAATATAATTTTTGA-AAAGT
* * *
44128248 TTATGGGTTAAAATATAATTTTTGAAAAGC
1 TTAGGGGTCAAAATATAATTTTTGAAAAGT
*
44128278 TTAGGGG-CTAAAATACAATTTTT
1 TTAGGGGTC-AAAATATAATTTTT
44128301 AATAAAATAA
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
29 1 0.01
30 97 0.98
31 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (30 bp):
TTAGGGGTCAAAATATAATTTTTGAAAAGT
Found at i:44130510 original size:49 final size:49
Alignment explanation
Indices: 44130454--44130879 Score: 480
Period size: 49 Copynumber: 8.7 Consensus size: 49
44130444 TTAAGGTATA
* * * *
44130454 AGATTCGTCGTTGTGGCTTCAATC-TTCTCCTTCATGTCTTCGTGGTACT
1 AGATTCGCCGTTGCGGCTTAAATCTTTC-CCTTCATATCTTCGTGGTACT
* * *
44130503 AGGTTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTCGTGGTACT
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATATCTTCGTGGTACT
* * *
44130552 AGATTCGCCGTTGCGGCTTAAATCTTTCCTTTTATATCTTTGTGGTACT
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATATCTTCGTGGTACT
* * * *
44130601 AGATTCGTCGTTGCGGCTTAAATCTTTCCTTTTATATCTTTGTGGTACT
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATATCTTCGTGGTACT
* * * *
44130650 AGATTCGCCGTTGCGGCCTAAATCTTTCCCTTCAT-GCTTCTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATATCTTC-GTGGTACT
* * * * * *
44130699 AGGTTCACCATTGCGACTTAAACCTTTCCCTTCACATCTTCGTGGTACT
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATATCTTCGTGGTACT
* * * * *
44130748 AGATTCGCCGTTGTGGTTTAAATCTTTCCCTTCAT-GCTTCTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATATCTTC-GTGGTACT
* * * * *
44130797 AGGTTCGCCGTTGTGACTTAAACCTTTCCCTTCATATCTTCATGGTACT
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATATCTTCGTGGTACT
* *
44130846 AGATTCGTCGTTGCGGTTTAAATCTTTCCCTTCA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCA
44130880 AACCTGCAGA
Statistics
Matches: 319, Mismatches: 53, Indels: 10
0.84 0.14 0.03
Matches are distributed among these distances:
48 7 0.02
49 301 0.94
50 11 0.03
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (49 bp):
AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATATCTTCGTGGTACT
Found at i:44140887 original size:258 final size:258
Alignment explanation
Indices: 44140430--44140928 Score: 917
Period size: 258 Copynumber: 1.9 Consensus size: 258
44140420 GATCCCTCAG
44140430 ACTCTTCCAAGTGATACATTTATTATCCCTTTTTACCTTGATCCTAGATACTACCCATTGTTAAC
1 ACTCTTCCAAGTGATACATTTATTATCCCTTTTTACCTTGATCCTAGATACTACCCATTGTTAAC
* * *
44140495 TCATCCCGGTTATATTCATCAACCTCTTGAGAAAGGTTGAGACACACGCAGCTCTTGAGTAAACC
66 TCATCCCGATTATATTCATCAACCTCTTGAGAAAGATCGAGACACACGCAGCTCTTGAGTAAACC
*
44140560 TTATCAACTTGAATCTTTGGGCAATGGATCAATGCGGTGTATTCCTCCACTGTAGGTGTCATGTC
131 TTATCAACTTGAATCTTTGAGCAATGGATCAATGCGGTGTATTCCTCCACTGTAGGTGTCATGTC
*
44140625 GAAATTCCAAAGGAAAAGCAACTATACGCAGTATTCCAGTGTTGGGCAATGGATAAATGTATC
196 GAAATTCCAAAGGAAAAGCAACTATACGCAGGATTCCAGTGTTGGGCAATGGATAAATGTATC
* *
44140688 ACTCTTCCAAGTGATACATTTATTATCCCTTTTTACTTTGATCCTAGATACTACCCATTGTTCAC
1 ACTCTTCCAAGTGATACATTTATTATCCCTTTTTACCTTGATCCTAGATACTACCCATTGTTAAC
* *
44140753 TCATCCCGATTATATTCATCAACCTTTTGAGAAAGATCGAGACACACGCAGCTCTTGAGTAGACC
66 TCATCCCGATTATATTCATCAACCTCTTGAGAAAGATCGAGACACACGCAGCTCTTGAGTAAACC
44140818 TTATCAACTTGAATCTTTGAGCAATGGATCAATGCGGTGTATTCCTCCACTGTAGGTGTCATGTC
131 TTATCAACTTGAATCTTTGAGCAATGGATCAATGCGGTGTATTCCTCCACTGTAGGTGTCATGTC
44140883 GAAATTCCAAAGGAAAAGCAACTATACGCAGGATTCCAGTGTTGGG
196 GAAATTCCAAAGGAAAAGCAACTATACGCAGGATTCCAGTGTTGGG
44140929 TGAGAGTTAG
Statistics
Matches: 232, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
258 232 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (258 bp):
ACTCTTCCAAGTGATACATTTATTATCCCTTTTTACCTTGATCCTAGATACTACCCATTGTTAAC
TCATCCCGATTATATTCATCAACCTCTTGAGAAAGATCGAGACACACGCAGCTCTTGAGTAAACC
TTATCAACTTGAATCTTTGAGCAATGGATCAATGCGGTGTATTCCTCCACTGTAGGTGTCATGTC
GAAATTCCAAAGGAAAAGCAACTATACGCAGGATTCCAGTGTTGGGCAATGGATAAATGTATC
Found at i:44142905 original size:30 final size:30
Alignment explanation
Indices: 44142866--44142968 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
44142856 AAAATGTAAA
*
44142866 TTTGGAAAGTTTAGGGGTCAAAATATAATT
1 TTTGAAAAGTTTAGGGGTCAAAATATAATT
** *
44142896 TTCAAAAAGTTTAGGGGTCAAAAAATAATT
1 TTTGAAAAGTTTAGGGGTCAAAATATAATT
* *
44142926 TTTGAAAAGTCTAGGAGTCAAAATATAATT
1 TTTGAAAAGTTTAGGGGTCAAAATATAATT
44142956 TTTGAAAAGTTTA
1 TTTGAAAAGTTTA
44142969 AAGGTTAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAAAGTTTAGGGGTCAAAATATAATT
Found at i:44142979 original size:30 final size:30
Alignment explanation
Indices: 44142866--44142980 Score: 133
Period size: 30 Copynumber: 3.8 Consensus size: 30
44142856 AAAATGTAAA
* *
44142866 TTTGGAAAGTTTAGGGGTCAAAATATAATT
1 TTTGAAAAGTTTAAGGGTCAAAATATAATT
** * *
44142896 TTCAAAAAGTTTAGGGGTCAAAAAATAATT
1 TTTGAAAAGTTTAAGGGTCAAAATATAATT
*
44142926 TTTGAAAAGTCT-AGGAGTCAAAATATAATT
1 TTTGAAAAGTTTAAGG-GTCAAAATATAATT
* *
44142956 TTTGAAAAGTTTAAAGGTTAAAATA
1 TTTGAAAAGTTTAAGGGTCAAAATA
44142981 CAGTTTTCGA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
29 2 0.03
30 67 0.94
31 2 0.03
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.34
Consensus pattern (30 bp):
TTTGAAAAGTTTAAGGGTCAAAATATAATT
Found at i:44144379 original size:20 final size:18
Alignment explanation
Indices: 44144329--44144367 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
44144319 GAGGAGTGCT
* *
44144329 TCGGGAAGAGGAGGGATC
1 TCGGGCAGAGGAGCGATC
44144347 TCGGGCAGAGGAGCGATC
1 TCGGGCAGAGGAGCGATC
44144365 TCG
1 TCG
44144368 AGAGCCGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.18, G:0.46, T:0.13
Consensus pattern (18 bp):
TCGGGCAGAGGAGCGATC
Found at i:44149545 original size:15 final size:15
Alignment explanation
Indices: 44149525--44149558 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
44149515 ATTTATAGTA
44149525 CTTTTAATTTAATAT
1 CTTTTAATTTAATAT
44149540 CTTTTAATTTAATAT
1 CTTTTAATTTAATAT
44149555 -TTTT
1 CTTTT
44149559 CATGTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (15 bp):
CTTTTAATTTAATAT
Found at i:44150380 original size:14 final size:15
Alignment explanation
Indices: 44150361--44150390 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
44150351 TAAAAGAGCA
44150361 ATTACCATA-ATATT
1 ATTACCATATATATT
44150375 ATTACCATATATATT
1 ATTACCATATATATT
44150390 A
1 A
44150391 AAGGCAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTACCATATATATT
Found at i:44150412 original size:47 final size:46
Alignment explanation
Indices: 44150346--44150513 Score: 191
Period size: 47 Copynumber: 3.6 Consensus size: 46
44150336 AATTTTATAT
*
44150346 GGTAATAAAAGAGCAATTACCATAATATTATTACCATATATATTAAA
1 GGTAATAAAA-AGAAATTACCATAATATTATTACCATATATATTAAA
* *
44150393 GGCAATAAAAAGAACATTACCATAATATTATTGCC--ATATA-T-AA
1 GGTAATAAAAAGAA-ATTACCATAATATTATTACCATATATATTAAA
* *
44150436 GGTAATAAAAAGAGTAATTACCAAAACATTATTACCATATATATTAAA
1 GGTAATAAAAAGA--AATTACCATAATATTATTACCATATATATTAAA
** *
44150484 ATTAATAAAAAGCAATTACCATATATATTA
1 GGTAATAAAAAGAAATTACCATA-ATATTA
44150514 AAATTAATAA
Statistics
Matches: 101, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
43 14 0.14
44 18 0.18
45 6 0.06
46 17 0.17
47 34 0.34
48 12 0.12
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (46 bp):
GGTAATAAAAAGAAATTACCATAATATTATTACCATATATATTAAA
Found at i:44150447 original size:91 final size:90
Alignment explanation
Indices: 44150341--44150513 Score: 249
Period size: 91 Copynumber: 1.9 Consensus size: 90
44150331 CAATTAATTT
* * * *
44150341 TATATGGTAATAAAAGAGCAATTACCATAATATTATTACCATATATATTAAAGGCAATAAAAAGA
1 TATAAGGTAATAAAAGAGCAATTACCAAAACATTATTACCATATATATTAAAAGCAATAAAAAGA
44150406 ACATTACCATA-ATATTATTGCCATA
66 A-ATTACCATATATATTATTGCCATA
* **
44150431 TATAAGGTAATAAAAAGAGTAATTACCAAAACATTATTACCATATATATTAAAATTAATAAAAAG
1 TATAAGGTAAT-AAAAGAGCAATTACCAAAACATTATTACCATATATATTAAAAGCAATAAAAAG
*
44150496 CAATTACCATATATATTA
65 AAATTACCATATATATTA
44150514 AAATTAATAA
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
90 19 0.26
91 54 0.74
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (90 bp):
TATAAGGTAATAAAAGAGCAATTACCAAAACATTATTACCATATATATTAAAAGCAATAAAAAGA
AATTACCATATATATTATTGCCATA
Found at i:44150458 original size:44 final size:43
Alignment explanation
Indices: 44150341--44150478 Score: 154
Period size: 44 Copynumber: 3.1 Consensus size: 43
44150331 CAATTAATTT
*
44150341 TATATGGTAAT-AAAAGAGCAATTACCATAATATTATTACCATATA
1 TATAAGGTAATAAAAAGAG-AATTACCATAATATTATTACC--ATA
* *
44150386 TATTAAAGGCAATAAAAAGA-ACATTACCATAATATTATTGCCATA
1 TA-T-AAGGTAATAAAAAGAGA-ATTACCATAATATTATTACCATA
* *
44150431 TATAAGGTAATAAAAAGAGTAATTACCAAAACATTATTACCATA
1 TATAAGGTAATAAAAAGAG-AATTACCATAATATTATTACCATA
44150475 TATA
1 TATA
44150479 TTAAAATTAA
Statistics
Matches: 80, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
43 14 0.17
44 25 0.31
45 8 0.10
46 2 0.03
47 25 0.31
48 6 0.08
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (43 bp):
TATAAGGTAATAAAAAGAGAATTACCATAATATTATTACCATA
Found at i:44150502 original size:32 final size:32
Alignment explanation
Indices: 44150466--44150639 Score: 296
Period size: 32 Copynumber: 5.4 Consensus size: 32
44150456 CCAAAACATT
44150466 ATTACCATATATATTAAAATTAATAAAAAGCA
1 ATTACCATATATATTAAAATTAATAAAAAGCA
44150498 ATTACCATATATATTAAAATTAATAAAAAGCA
1 ATTACCATATATATTAAAATTAATAAAAAGCA
44150530 ATTACCATATATATTAAAA-TAATAAAAAAGCA
1 ATTACCATATATATTAAAATTAAT-AAAAAGCA
* * *
44150562 ATTACCATGTATATTAAAATGATTAAAAAGCA
1 ATTACCATATATATTAAAATTAATAAAAAGCA
*
44150594 ATTACCATGTATATTAAAATTAATAAAAAGCA
1 ATTACCATATATATTAAAATTAATAAAAAGCA
44150626 ATTACCATATATAT
1 ATTACCATATATAT
44150640 ATATATATCA
Statistics
Matches: 134, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
31 4 0.03
32 128 0.96
33 2 0.01
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.32
Consensus pattern (32 bp):
ATTACCATATATATTAAAATTAATAAAAAGCA
Found at i:44153626 original size:7 final size:7
Alignment explanation
Indices: 44153614--44153646 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
44153604 GCTATCACAG
44153614 TCATGCA
1 TCATGCA
44153621 TCATGCA
1 TCATGCA
44153628 TCATGCA
1 TCATGCA
44153635 TCATGCA
1 TCATGCA
44153642 T-ATGC
1 TCATGC
44153647 CTACCATCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.15
7 22 0.85
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (7 bp):
TCATGCA
Found at i:44160649 original size:91 final size:91
Alignment explanation
Indices: 44160494--44160675 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
44160484 CTGGGTAATT
44160494 GGTTAATTTCAATAAGTCTATACTCCTTTCCTCAGAAAATACCCTCTCTTGGTGTGCTTTGTGGG
1 GGTTAATTTCAATAAGTCTATACTCCTTTCCTCAGAAAATACCCTCTCTTGGTGTGCTTTGTGGG
44160559 GTATGCTTGGAGTCAATTATATGAGA
66 GTATGCTTGGAGTCAATTATATGAGA
44160585 GGTTAATTTCAATAAGTCTATACTCCTTTCCTCAGAAAATACCCTCTCTTGGTGTGCTTTGTGGG
1 GGTTAATTTCAATAAGTCTATACTCCTTTCCTCAGAAAATACCCTCTCTTGGTGTGCTTTGTGGG
44160650 GTATGCTTGGAGTCAATTATATGAGA
66 GTATGCTTGGAGTCAATTATATGAGA
44160676 TGTGACTCTA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (91 bp):
GGTTAATTTCAATAAGTCTATACTCCTTTCCTCAGAAAATACCCTCTCTTGGTGTGCTTTGTGGG
GTATGCTTGGAGTCAATTATATGAGA
Found at i:44162189 original size:26 final size:27
Alignment explanation
Indices: 44162141--44162191 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
44162131 GCCATTAAAA
*
44162141 ATTTAAAATAATATCCATTTAATAATT
1 ATTTAAAATAATATACATTTAATAATT
44162168 ATTTAAAA-AATA-ACATTATAATAA
1 ATTTAAAATAATATACATT-TAATAA
44162192 ACTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 10 0.45
27 8 0.36
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (27 bp):
ATTTAAAATAATATACATTTAATAATT
Found at i:44162578 original size:42 final size:42
Alignment explanation
Indices: 44162517--44162604 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
44162507 TTTATGTTCG
* *
44162517 TTTAATAAATGAACGAACACGAACAAAGGTGTATTAGATTCA
1 TTTAATAAACGAACAAACACGAACAAAGGTGTATTAGATTCA
* * * *
44162559 TTTAATAAACGAACAAACACGAACAGAGGTGTGTTCGATTCG
1 TTTAATAAACGAACAAACACGAACAAAGGTGTATTAGATTCA
44162601 TTTA
1 TTTA
44162605 TGTTCACGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (42 bp):
TTTAATAAACGAACAAACACGAACAAAGGTGTATTAGATTCA
Found at i:44174597 original size:40 final size:41
Alignment explanation
Indices: 44174541--44174619 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 41
44174531 TAAACTAGGC
44174541 CAGGGAATATTGACATTGAAACAACAATTTACGAGTTACCA
1 CAGGGAATATTGACATTGAAACAACAATTTACGAGTTACCA
* *
44174582 CAGGG-ATATTGACATTGAAACAACAGTTTAGGAGTTAC
1 CAGGGAATATTGACATTGAAACAACAATTTACGAGTTAC
44174620 TAACCTGACA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 31 0.86
41 5 0.14
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.25
Consensus pattern (41 bp):
CAGGGAATATTGACATTGAAACAACAATTTACGAGTTACCA
Done.