Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 137 of 175
Found at i:42373003 original size:18 final size:19
Alignment explanation
Indices: 42372982--42373051 Score: 56
Period size: 19 Copynumber: 3.7 Consensus size: 19
42372972 ATTCATGTAA
42372982 TTTTATA-ATTTTTTACAC
1 TTTTATATATTTTTTACAC
* * * *
42373000 TTTTTTATATTTTATAATAT
1 TTTTATATATTTT-TTACAC
*
42373020 TTTTA-AT-TATTTTTGCAC
1 TTTTATATAT-TTTTTACAC
42373038 TTTTATATATTTTT
1 TTTTATATATTTTT
42373052 ATAGTTTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
18 14 0.37
19 16 0.42
20 8 0.21
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTTATATATTTTTTACAC
Found at i:42373024 original size:38 final size:39
Alignment explanation
Indices: 42372982--42373107 Score: 111
Period size: 38 Copynumber: 3.3 Consensus size: 39
42372972 ATTCATGTAA
42372982 TTTTATAATTTTTTACACTTTTTTATA-TTTTATAATAT
1 TTTTATAATTTTTTACACTTTTTTATATTTTTATAATAT
* * * *
42373020 TTTTA-ATTATTTTTGCACTTTTATATATTTTTATAGT-T
1 TTTTATAAT-TTTTTACACTTTTTTATATTTTTATAATAT
* * *
42373058 TTTTGTAA-TTTGTA-A-TTTTTTATTATTTTTTAAAATAT
1 TTTTATAATTTTTTACACTTTTTTA-TA-TTTTTATAATAT
*
42373096 TTTTATGATTTT
1 TTTTATAATTTT
42373108 AAGTATAAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
35 6 0.09
36 3 0.04
37 14 0.21
38 33 0.49
39 12 0.18
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (39 bp):
TTTTATAATTTTTTACACTTTTTTATATTTTTATAATAT
Found at i:42373032 original size:28 final size:27
Alignment explanation
Indices: 42372981--42373088 Score: 85
Period size: 28 Copynumber: 3.9 Consensus size: 27
42372971 AATTCATGTA
* *
42372981 ATTTTATAATTTTTTACACTTTTTTAT
1 ATTTTATAATTTTTTACATTTTTTTGT
*
42373008 ATTTTATAATATTTTTA-ATTATTTTTGC
1 ATTTTATAAT-TTTTTACATT-TTTTTGT
* *
42373036 ACTTTTAT-ATATTTTTATAGTTTTTTGT
1 A-TTTTATAAT-TTTTTACATTTTTTTGT
* * *
42373064 AATTTGTAATTTTTTATTATTTTTT
1 ATTTTATAATTTTTTA-CATTTTTT
42373089 AAAATATTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
27 22 0.33
28 37 0.55
29 8 0.12
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (27 bp):
ATTTTATAATTTTTTACATTTTTTTGT
Found at i:42379780 original size:16 final size:16
Alignment explanation
Indices: 42379759--42379799 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
42379749 GATAATGAAT
*
42379759 TTTAATTTTT-TTTATA
1 TTTAATTTTTATTT-GA
42379775 TTTAATTTTTATTTGA
1 TTTAATTTTTATTTGA
42379791 TTTAATTTT
1 TTTAATTTT
42379800 CACAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTAATTTTTATTTGA
Found at i:42391386 original size:85 final size:84
Alignment explanation
Indices: 42391283--42391441 Score: 237
Period size: 85 Copynumber: 1.9 Consensus size: 84
42391273 GAAATTAAAA
* * * *
42391283 TTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGATTAACAAGATTTTATTCGATTTTAATTTT
1 TTAAATAAAATCTATTTCGAGATTTATTCCCGCCGATTAACAAGATTTTATTCAATATTAA-TTT
42391348 ATTTCCAAATTAGAATTAAT
65 ATTTCCAAATTAGAATTAAT
* * * *
42391368 TTAAATAAAATCTATTTCGAGATTTATTCCCGTCGTTTAAGAAGATTTTATTCAATATTAATTTG
1 TTAAATAAAATCTATTTCGAGATTTATTCCCGCCGATTAACAAGATTTTATTCAATATTAATTTA
42391433 TTTCCAAAT
66 TTTCCAAAT
42391442 GAAGACTTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 12 0.18
85 54 0.82
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (84 bp):
TTAAATAAAATCTATTTCGAGATTTATTCCCGCCGATTAACAAGATTTTATTCAATATTAATTTA
TTTCCAAATTAGAATTAAT
Found at i:42396434 original size:14 final size:14
Alignment explanation
Indices: 42396415--42396459 Score: 65
Period size: 13 Copynumber: 3.2 Consensus size: 14
42396405 AATCATTCTA
42396415 TTTATATATTTTAT
1 TTTATATATTTTAT
42396429 TTTATATA-TTTAT
1 TTTATATATTTTAT
*
42396442 TTTATATTTATTTAT
1 TTTATATAT-TTTAT
42396457 TTT
1 TTT
42396460 GTTCGATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 12 0.43
14 8 0.29
15 8 0.29
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATATATTTTAT
Found at i:42397132 original size:21 final size:21
Alignment explanation
Indices: 42397108--42397149 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
42397098 CCTTAACTTA
42397108 AATTGTTCATC-TCCTCTTTTT
1 AATTGTTCATCGT-CTCTTTTT
* *
42397129 AATTTTTCTTCGTCTCTTTTT
1 AATTGTTCATCGTCTCTTTTT
42397150 TTTTAGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.12, C:0.21, G:0.05, T:0.62
Consensus pattern (21 bp):
AATTGTTCATCGTCTCTTTTT
Found at i:42405540 original size:2 final size:2
Alignment explanation
Indices: 42405535--42405572 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
42405525 AAAAAAAGAA
42405535 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
42405573 GGGGGGGGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42407071 original size:3 final size:3
Alignment explanation
Indices: 42407063--42407094 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42407053 TTTTTAATAT
42407063 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42407095 TTACAAGTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:42411428 original size:17 final size:17
Alignment explanation
Indices: 42411406--42411439 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
42411396 GAGTAATATG
42411406 AAATTGTGACTTTAGGT
1 AAATTGTGACTTTAGGT
42411423 AAATTGTGACTTTAGGT
1 AAATTGTGACTTTAGGT
42411440 TTACATGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (17 bp):
AAATTGTGACTTTAGGT
Found at i:42413112 original size:90 final size:90
Alignment explanation
Indices: 42412854--42413113 Score: 326
Period size: 89 Copynumber: 2.9 Consensus size: 90
42412844 ATTTGCAGCT
** * *
42412854 CTGGTGGTTCATCCATAGA-TTTCTGACAGCTCTTATCTACAAATATGTTATGCATTCACAACCA
1 CTGGTGGTTCATCCATCCATTTTCTGGCAGCTCTTATATACAAATATGTTATGCATTCACAACCA
42412918 TCTGGCAGCGTATTAACCTGCAACA
66 TCTGGCAGCGTATTAACCTGCAACA
* * * * ** *
42412943 CTGGTGGTTCATCAACCCATTTT-TTGCAGCTCTTATGTGTAAATATGTTCTGCATTCACAACCA
1 CTGGTGGTTCATCCATCCATTTTCTGGCAGCTCTTATATACAAATATGTTATGCATTCACAACCA
* * *
42413007 TCTGACAACGTATTAATCTGCAACA
66 TCTGGCAGCGTATTAACCTGCAACA
* * * *
42413032 CTGGTGGTTCACCCATCCATTTTCTGGCAGCTCTCATATACAAATATGTTGTGCATTCACAACCG
1 CTGGTGGTTCATCCATCCATTTTCTGGCAGCTCTTATATACAAATATGTTATGCATTCACAACCA
* *
42413097 TTTGGCAGCGAATTAAC
66 TCTGGCAGCGTATTAAC
42413114 ATACAAATTT
Statistics
Matches: 141, Mismatches: 28, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
89 92 0.65
90 49 0.35
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (90 bp):
CTGGTGGTTCATCCATCCATTTTCTGGCAGCTCTTATATACAAATATGTTATGCATTCACAACCA
TCTGGCAGCGTATTAACCTGCAACA
Found at i:42416170 original size:14 final size:14
Alignment explanation
Indices: 42416148--42416187 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
42416138 CATTGATCTA
42416148 TAAAATAATTAAAT
1 TAAAATAATTAAAT
*
42416162 TAAATTAATTAAAT
1 TAAAATAATTAAAT
42416176 TAAAATATATTA
1 TAAAATA-ATTA
42416188 TCATATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAAATAATTAAAT
Found at i:42417874 original size:17 final size:18
Alignment explanation
Indices: 42417841--42417874 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42417831 TACTTCTTAT
42417841 GTATAAAAAACTTAAGTA
1 GTATAAAAAACTTAAGTA
*
42417859 GTATATAAAA-TTAAGT
1 GTATAAAAAACTTAAGT
42417875 TTTGTCTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (18 bp):
GTATAAAAAACTTAAGTA
Found at i:42418245 original size:21 final size:21
Alignment explanation
Indices: 42418219--42418294 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 21
42418209 TACGAGGAGG
42418219 ATTCATTGTTATGATTTCGATATT
1 ATTCATTGTTATGATTTCG--A-T
* *
42418243 CATTCAATTTTTATGATTTTCTG-G
1 -ATTC-ATTGTTATGA-TTTC-GAT
42418267 ATTCATTGTTATGATTTCGAT
1 ATTCATTGTTATGATTTCGAT
42418288 ATTCATT
1 ATTCATT
42418295 CAATTTTTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
20 1 0.02
21 11 0.26
22 9 0.21
23 4 0.09
25 4 0.09
26 9 0.21
27 4 0.09
28 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.12, T:0.54
Consensus pattern (21 bp):
ATTCATTGTTATGATTTCGAT
Found at i:42418644 original size:16 final size:18
Alignment explanation
Indices: 42418615--42418659 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
42418605 TAAAAATTAT
42418615 AAATTAA-A-TTTTATT-
1 AAATTAATATTTTTATTC
42418630 AAA-TAATATTTTTATTC
1 AAATTAATATTTTTATTC
42418647 AAATTAATATTTT
1 AAATTAATATTTT
42418660 GAAATATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.12
15 4 0.15
16 7 0.27
17 3 0.12
18 9 0.35
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATTAATATTTTTATTC
Found at i:42419781 original size:17 final size:16
Alignment explanation
Indices: 42419755--42419786 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
42419745 GTGCTTTTCT
42419755 AAAACACTTCTGAAAG
1 AAAACACTTCTGAAAG
42419771 AAAATCACTTCTGAAA
1 AAAA-CACTTCTGAAA
42419787 AGGAGAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.19, G:0.09, T:0.22
Consensus pattern (16 bp):
AAAACACTTCTGAAAG
Found at i:42420272 original size:13 final size:13
Alignment explanation
Indices: 42420256--42420308 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
42420246 TTTAAACCAA
42420256 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
* * *
42420269 ACTTTCCCACAAC
1 ACTTTTCAAAAAC
42420282 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
42420295 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
42420308 A
1 A
42420309 ATGAAAAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:42423978 original size:46 final size:45
Alignment explanation
Indices: 42423911--42424281 Score: 460
Period size: 46 Copynumber: 8.6 Consensus size: 45
42423901 TTTGAGTACT
*
42423911 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
42423957 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
42424003 TCTGATCAAGTGAAAAAGTGATAA---GT-G--T---TACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
42424039 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
42424085 TCTGATCAAGTGA-AAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
42424120 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* * *
42424166 TCTGATCAAGTGAGAAAGTTATAAGTGGTAGCCTTAGCTACTCTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
42424212 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
42424257 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
42424282 ATCATATGTA
Statistics
Matches: 289, Mismatches: 15, Indels: 45
0.83 0.04 0.13
Matches are distributed among these distances:
35 18 0.06
36 40 0.14
37 1 0.00
39 6 0.02
40 2 0.01
41 3 0.01
42 5 0.02
43 15 0.05
44 6 0.02
45 29 0.10
46 164 0.57
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:42424036 original size:36 final size:36
Alignment explanation
Indices: 42423995--42424149 Score: 168
Period size: 36 Copynumber: 4.1 Consensus size: 36
42423985 TAGCATTAGC
42423995 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
1 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
* *
42424031 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 TACACTTATCTGATCAAGTGAAAAAGTGATAA---GT-G---T
*
42424074 AGCTACACTTATCTGATCAAGTG-AAAAGTGATAAGTGC
1 ---TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
* *
42424112 TATACTTATCTGATCAAGTGACAAAGTGATAAGTGT
1 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
42424148 TA
1 TA
42424150 GCCTTAGCTA
Statistics
Matches: 100, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
35 19 0.19
36 45 0.45
39 2 0.02
40 1 0.01
41 1 0.01
42 2 0.02
43 1 0.01
45 10 0.10
46 19 0.19
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (36 bp):
TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
Found at i:42424042 original size:82 final size:81
Alignment explanation
Indices: 42423949--42424281 Score: 438
Period size: 81 Copynumber: 4.0 Consensus size: 81
42423939 TAGCATTAGC
*
42423949 TACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGT
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGT
42424014 GAAAAAGTGATAAGTGT
65 GAAAAAGTGATAAGTGT
*
42424031 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGT
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGT
*
42424096 G-AAAAGTGATAAGTGC
65 GAAAAAGTGATAAGTGT
* *
42424112 TATACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGT
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAAGT
* *
42424177 GAGAAAGTTATAAGTGGTAGCCT
65 GAAAAAGTGATAA---GT-G--T
*
42424200 TAGCTACTCTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-
1 TA-C-A--CTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCA
* *
42424264 AG-GGACAAGTGATAAGTG
62 AGTGAAAAAGTGATAAGTG
42424282 ATCATATGTA
Statistics
Matches: 222, Mismatches: 17, Indels: 21
0.85 0.07 0.08
Matches are distributed among these distances:
81 75 0.34
82 73 0.33
85 3 0.01
86 3 0.01
88 2 0.01
89 9 0.04
90 3 0.01
91 20 0.09
92 34 0.15
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (81 bp):
TACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTG
AAAAAGTGATAAGTGT
Found at i:42424125 original size:35 final size:36
Alignment explanation
Indices: 42424075--42424146 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 36
42424065 GGTAGCTTTA
42424075 GCTACACTTATCTGATCAAGTGA-AAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
*
42424110 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
42424146 G
1 G
42424147 TTAGCCTTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 22 0.63
36 13 0.37
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
Found at i:42427212 original size:19 final size:20
Alignment explanation
Indices: 42427184--42427222 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
42427174 GCTCATCTCA
*
42427184 ATGCATATTTCGT-AAAACG
1 ATGCAGATTTCGTGAAAACG
*
42427203 ATGCAGATTTTGTGAAAACG
1 ATGCAGATTTCGTGAAAACG
42427223 GTCTTACCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGCAGATTTCGTGAAAACG
Found at i:42440958 original size:37 final size:37
Alignment explanation
Indices: 42440895--42440970 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
42440885 AGATTATCAC
*
42440895 TTTAATATTAAATTAATAAAATACTATTAAGATAAGTA
1 TTTAATATTAAATTAATAAAATACTATTAAAATAA-TA
* *
42440933 TTTAAT-TTAATTTAATATTAA-ACTATTAAAATAATA
1 TTTAATATTAAATTAATA-AAATACTATTAAAATAATA
42440969 TT
1 TT
42440971 ATTTCTAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 4 0.12
37 22 0.65
38 8 0.24
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:42442605 original size:16 final size:16
Alignment explanation
Indices: 42442584--42442614 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42442574 CTATGAGTGC
*
42442584 AAAATATAAAAGACAA
1 AAAATACAAAAGACAA
42442600 AAAATACAAAAGACA
1 AAAATACAAAAGACA
42442615 TAATAATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAA
Found at i:42443549 original size:6 final size:6
Alignment explanation
Indices: 42443538--42443565 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
42443528 TAAAGTTCGT
42443538 ATATAC ATATAC ATATAC ATATAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATAT
42443566 TTTAATAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAC
Found at i:42443866 original size:23 final size:24
Alignment explanation
Indices: 42443790--42443865 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
42443780 TTATAAGATT
* ***
42443790 AAAAAATTTAGTAATCAAT-CCCC
1 AAAAAATTTATTAATCAATATATC
* *
42443813 AAAAAAATTGTTAATCAATATATC
1 AAAAAATTTATTAATCAATATATC
*
42443837 AAAAAATTTATTAATCAATATATG
1 AAAAAATTTATTAATCAATATATC
42443861 AAAAA
1 AAAAA
42443866 TTGATTTTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 16 0.37
24 27 0.63
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (24 bp):
AAAAAATTTATTAATCAATATATC
Found at i:42446880 original size:22 final size:22
Alignment explanation
Indices: 42446862--42446944 Score: 98
Period size: 22 Copynumber: 3.8 Consensus size: 22
42446852 ATTAATTTCT
42446862 TTCAAAAATTCTCTCAATT-CC
1 TTCAAAAATTCTCTCAATTCCC
*
42446883 TTTAAAAATTTCTCTCAATTCCC
1 TTCAAAAA-TTCTCTCAATTCCC
* *
42446906 TTCAAAATTTC-CATCAATTTCC
1 TTCAAAAATTCTC-TCAATTCCC
*
42446928 TTCCAAAATTCTCTCAA
1 TTCAAAAATTCTCTCAA
42446945 ACTCTCAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
21 8 0.15
22 35 0.67
23 9 0.17
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCAAAAATTCTCTCAATTCCC
Found at i:42446951 original size:52 final size:50
Alignment explanation
Indices: 42446894--42446995 Score: 120
Period size: 52 Copynumber: 2.0 Consensus size: 50
42446884 TTAAAAATTT
*
42446894 CTCTC-AATTCCCTT-CAAAATTTCC-ATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATT-CCTTCCAAAA--TCCTATCAATTTCCTT-CAAAAATCTC-CAAA
*
42446946 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAATCTCCAAA
1 CTCTCAAATTCCTTCCAAAATCCTATCAATTTCCTTCAAAAATCTCCAAA
42446996 TCCATATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
50 4 0.09
51 12 0.27
52 20 0.44
53 9 0.20
ACGTcount: A:0.32, C:0.33, G:0.00, T:0.34
Consensus pattern (50 bp):
CTCTCAAATTCCTTCCAAAATCCTATCAATTTCCTTCAAAAATCTCCAAA
Found at i:42446985 original size:21 final size:22
Alignment explanation
Indices: 42446946--42446996 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
42446936 TTCTCTCAAA
42446946 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
42446968 CTCTCAATTTCCTTCAAAAAT-
1 CTCTCAAATTCCTTCCAAAATC
42446989 CTC-CAAAT
1 CTCTCAAAT
42446997 CCATATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 4 0.15
21 3 0.12
22 19 0.73
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:42447090 original size:29 final size:30
Alignment explanation
Indices: 42447028--42447090 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 30
42447018 ATTAAATTTC
*
42447028 ATTTTTTAAGAAAATTTTAAAATTTTTTAT
1 ATTTTTTAAGAAAATTTTAAAATTTTTAAT
*
42447058 -TTTTTTAA-ATAATTTTAAAATTTTTAAT
1 ATTTTTTAAGAAAATTTTAAAATTTTTAAT
42447086 ATTTT
1 ATTTT
42447091 CAACAATGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
ATTTTTTAAGAAAATTTTAAAATTTTTAAT
Found at i:42447235 original size:24 final size:23
Alignment explanation
Indices: 42447180--42447235 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
42447170 TTAATTTTAA
*
42447180 ATTTTTTTAAGATATTTTTATTT
1 ATTTTTTTAAGATATTTTTATAT
42447203 ATCTATTTTT-AGATATTTATTAATAT
1 AT-T-TTTTTAAGATATTT-TT-ATAT
42447229 ATTTTTT
1 ATTTTTT
42447236 GTTATAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 13 0.46
25 8 0.29
26 5 0.18
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.66
Consensus pattern (23 bp):
ATTTTTTTAAGATATTTTTATAT
Found at i:42449388 original size:17 final size:18
Alignment explanation
Indices: 42449366--42449401 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42449356 TAAAATCCCT
42449366 AAACCCT-ACTTAATTAA
1 AAACCCTAACTTAATTAA
*
42449383 AAACCCTAATTTAATTAA
1 AAACCCTAACTTAATTAA
42449401 A
1 A
42449402 TTAAAAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (18 bp):
AAACCCTAACTTAATTAA
Found at i:42449407 original size:23 final size:23
Alignment explanation
Indices: 42449377--42449489 Score: 111
Period size: 23 Copynumber: 4.7 Consensus size: 23
42449367 AACCCTACTT
*
42449377 AATTAAAAACCCTAATTTAATTA
1 AATTAAAAACCCTAATCTAATTA
* * *
42449400 AATTAAAAACTCTAACCTAATTT
1 AATTAAAAACCCTAATCTAATTA
42449423 AATTAAAAACCCTAACCTAACCTAATTA
1 AATTAAAAACCCTAA--T---CTAATTA
* *
42449451 AATTAAAAACCCTAACCCT-ATTT
1 AATTAAAAACCCTAA-TCTAATTA
42449474 AATTAAAAACCCTAAT
1 AATTAAAAACCCTAAT
42449490 TAAATTGTAG
Statistics
Matches: 75, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
23 51 0.68
24 2 0.03
27 1 0.01
28 21 0.28
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (23 bp):
AATTAAAAACCCTAATCTAATTA
Found at i:42449418 original size:28 final size:28
Alignment explanation
Indices: 42449387--42449480 Score: 110
Period size: 28 Copynumber: 3.5 Consensus size: 28
42449377 AATTAAAAAC
*
42449387 CCTAATTTAATTAAATTAAAAACTCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
42449415 CCTAA--T--TT-AATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
**
42449438 CCTAACCTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
42449466 CCCT-ATTTAATTAAA
1 -CCTAATTTAATTAAA
42449481 AACCCTAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
23 19 0.33
24 2 0.04
25 1 0.02
26 1 0.02
27 2 0.04
28 29 0.51
29 3 0.05
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (28 bp):
CCTAATTTAATTAAATTAAAAACCCTAA
Found at i:42452797 original size:83 final size:84
Alignment explanation
Indices: 42452599--42452800 Score: 379
Period size: 83 Copynumber: 2.4 Consensus size: 84
42452589 CAAACTTGCT
42452599 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
1 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
42452664 ATTATTTCCTACATGACCA
66 ATTATTTCCTACATGACCA
* *
42452683 ACTGTAGCAAAATCGCGTCCACGAGGTCGCGATTTGACACTATTTGCTCAGAAACGTC-AAAAAA
1 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
42452747 ATTATTTCCTACATGACCA
66 ATTATTTCCTACATGACCA
42452766 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTT
1 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTT
42452801 CACAATTTCT
Statistics
Matches: 114, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 58 0.51
84 56 0.49
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (84 bp):
ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
ATTATTTCCTACATGACCA
Found at i:42452930 original size:124 final size:123
Alignment explanation
Indices: 42452711--42452989 Score: 366
Period size: 124 Copynumber: 2.3 Consensus size: 123
42452701 CCACGAGGTC
*
42452711 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAATTATTTCCTACATGACCAACTGTAGCGA
1 GCGATTTGACACTATTTCCTCAGAAACGTCAAAAAAATTATTTCCTACATGACCAACTGTAGCGA
* * * * * **
42452776 AATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 AATCGCGTCCACGAGGCCACGATGTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
* *
42452834 GCGATTTTATACTATTTCCTCAGAAAACGTCAAAAAAAATTATTT-CTCACATGACC-ACTGTAG
1 GCGATTTGACACTATTTCCTCAG-AAACGTC-AAAAAAATTATTTCCT-ACATGACCAACTGTAG
* *
42452897 CGAAATCGCGTCCACGAGGCCACTATGTCACAATTTCTTCTTAAATAGCATCCTAGTAGAA
63 CGAAATCGCGTCCACGAGGCCACGATGTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
** *
42452958 GCGATTTCCCACTATTTAAC-CAGAAACGTCAA
1 GCGATTTGACACTATTT-CCTCAGAAACGTCAA
42452990 CTCAAAAAAA
Statistics
Matches: 136, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
122 2 0.01
123 27 0.20
124 85 0.62
125 22 0.16
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.28
Consensus pattern (123 bp):
GCGATTTGACACTATTTCCTCAGAAACGTCAAAAAAATTATTTCCTACATGACCAACTGTAGCGA
AATCGCGTCCACGAGGCCACGATGTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
Found at i:42455866 original size:18 final size:18
Alignment explanation
Indices: 42455817--42455866 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
42455807 AAAAAAAATG
*
42455817 TTTTGAAATTGAATAACA
1 TTTTGAAAATGAATAACA
* * *
42455835 ATTTGTAAATGAATAATA
1 TTTTGAAAATGAATAACA
*
42455853 TTTTGAAAACGAAT
1 TTTTGAAAATGAAT
42455867 GACACGATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (18 bp):
TTTTGAAAATGAATAACA
Found at i:42457852 original size:41 final size:41
Alignment explanation
Indices: 42457807--42457902 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
42457797 GAACACTGGA
* *
42457807 ATTAAGCCTGCTAGACATAAAGTCTGAAATATTTCACCGGC
1 ATTAAGCCTGCTAGACATAAAGTATGAAATATTTCACCAGC
* *
42457848 ATTAAGCCTGTTAGACGTAAAGTATGAAATATTTCACCAGC
1 ATTAAGCCTGCTAGACATAAAGTATGAAATATTTCACCAGC
*
42457889 ATTAAACCTGCTAG
1 ATTAAGCCTGCTAG
42457903 GCACAGAGCC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (41 bp):
ATTAAGCCTGCTAGACATAAAGTATGAAATATTTCACCAGC
Found at i:42458308 original size:65 final size:67
Alignment explanation
Indices: 42458183--42458336 Score: 172
Period size: 65 Copynumber: 2.3 Consensus size: 67
42458173 TCTTATATAT
* **
42458183 ATATATATATATATATTTCATAACATTACATTCAATTCAAAGACATTGCATCATTTATTCGAAC-
1 ATATATATATATA-ATTT-ATAACATTACATTCAACTCAAAGACATTGCATCATACATTCGAACA
42458247 CA-C
64 CATC
* * *
42458250 ATATATATATACAATTTATAACATTA-AGTTCAACTCAAAGA-ATTTGTATTATACATTCGAACA
1 ATATATATATATAATTTATAACATTACA-TTCAACTCAAAGACA-TTGCATCATACATTCGAACA
42458313 TCATC
64 -CATC
*
42458318 ATATATTTATATAATTTAT
1 ATATATATATATAATTTAT
42458337 GCTATTAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
64 2 0.03
65 36 0.49
66 4 0.05
67 14 0.19
68 18 0.24
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (67 bp):
ATATATATATATAATTTATAACATTACATTCAACTCAAAGACATTGCATCATACATTCGAACACA
TC
Found at i:42461000 original size:6 final size:6
Alignment explanation
Indices: 42460989--42461018 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
42460979 AATAATTGTA
42460989 AATTAT AATTAT AATTAT AATTAT AATTAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT
42461019 CACAAGTTTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTAT
Found at i:42462126 original size:21 final size:21
Alignment explanation
Indices: 42462100--42462140 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42462090 TCAAAAGCTG
*
42462100 AACAGAAGCTCGTGAGAGTTA
1 AACAGAAGCTCGTAAGAGTTA
42462121 AACAGAAGCTCGTAAGAGTT
1 AACAGAAGCTCGTAAGAGTT
42462141 GATCCACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.20
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGTTA
Found at i:42465547 original size:34 final size:34
Alignment explanation
Indices: 42465503--42465570 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
42465493 GCACAGTTGA
* *
42465503 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTA-CAGTG
*
42465538 ACAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
42465571 TTAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
Found at i:42472713 original size:67 final size:67
Alignment explanation
Indices: 42472629--42472786 Score: 280
Period size: 67 Copynumber: 2.4 Consensus size: 67
42472619 TCTGGTTCTA
*
42472629 CCGATGAAGCACTGGGTGCCAAACACACTAATGAGCACTGAGTGCAAACTATTTACCTCGGCATT
1 CCGATGAGGCACTGGGTGCCAAACACACTAATGAGCACTGAGTGCAAACTATTTACCTCGGCATT
42472694 GT
66 GT
*
42472696 CCGATGAGGCACTGGGTGCCAAACACACTAATGATCACTGAGTGCAAACTATTTACCTCGGCATT
1 CCGATGAGGCACTGGGTGCCAAACACACTAATGAGCACTGAGTGCAAACTATTTACCTCGGCATT
42472761 GT
66 GT
* *
42472763 CCGATGAGGCATTGGGTGTCAAAC
1 CCGATGAGGCACTGGGTGCCAAAC
42472787 TAGTGTAATT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 87 1.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (67 bp):
CCGATGAGGCACTGGGTGCCAAACACACTAATGAGCACTGAGTGCAAACTATTTACCTCGGCATT
GT
Found at i:42477999 original size:5 final size:5
Alignment explanation
Indices: 42477991--42478028 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
42477981 TATAGATACT
42477991 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT- TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
42478029 TTCTCTCGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:42478546 original size:7 final size:7
Alignment explanation
Indices: 42478530--42478563 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
42478520 GTTCTTTAAA
42478530 CTTTTCTT
1 CTTTT-TT
42478538 CTTTTTT
1 CTTTTTT
42478545 CTTTTTT
1 CTTTTTT
42478552 CTTTTTT
1 CTTTTTT
42478559 -TTTTT
1 CTTTTT
42478564 CATTCTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 5 0.19
7 16 0.62
8 5 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
CTTTTTT
Found at i:42478574 original size:17 final size:15
Alignment explanation
Indices: 42478530--42478574 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
42478520 GTTCTTTAAA
42478530 CTTTTCTTCTTTTTT
1 CTTTTCTTCTTTTTT
42478545 CTTTT-TTCTTTTTT
1 CTTTTCTTCTTTTTT
* *
42478559 TTTTTCATTCTATTTT
1 CTTTTC-TTCTTTTTT
42478575 ACTTATCCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 13 0.50
15 5 0.19
16 8 0.31
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (15 bp):
CTTTTCTTCTTTTTT
Found at i:42482508 original size:5 final size:5
Alignment explanation
Indices: 42482500--42482532 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
42482490 TATAAAATAA
42482500 TTATT TTA-- TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT
42482533 CATTTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.12
5 23 0.88
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:42482528 original size:23 final size:24
Alignment explanation
Indices: 42482500--42482546 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42482490 TATAAAATAA
* *
42482500 TTATTTTATT-ATTTTATTTTATT
1 TTATTTTATTCATTTAATTATATT
42482523 TTATTTTATTCATTTAATTATATT
1 TTATTTTATTCATTTAATTATATT
42482547 AAACTTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (24 bp):
TTATTTTATTCATTTAATTATATT
Found at i:42488499 original size:62 final size:59
Alignment explanation
Indices: 42488431--42488547 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
42488421 AGTGATTATC
* * * *
42488431 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTAACTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTCATC-T-T-GATAAATATTATATTAACTTAATAAGAT
*
42488493 TTAATATTAAATTTAATCTAATATTCATCTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTCATCTTGATAAATATTATATTAACTTAATA
42488548 TTAATATGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 22 0.44
60 1 0.02
61 1 0.02
62 26 0.52
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTCATCTTGATAAATATTATATTAACTTAATAAGAT
Found at i:42493554 original size:132 final size:131
Alignment explanation
Indices: 42493418--42494612 Score: 1639
Period size: 132 Copynumber: 9.1 Consensus size: 131
42493408 TGGGGTCTTC
* * * * ** * * *
42493418 GATCTGCTCCATTATTGCCTAGAGAGGTAAGATCTGTAATCTTCAATATATTCCACTGCTGCCTA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCC-A
* * **
42493483 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCTGTTATCC
65 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCC
42493548 TT
130 TT
* * * * *
42493550 GATCTGCTCCACTACTACTTAGGGAGACAAGATCTAAAATATTGAATCTATTCCACTGCTGCCCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CCA
* * * *
42493615 GGGAAGTAGAATTACTGGCTTCAATGTACTCCTCTATATCCACAGGGAGGTAAAAT-TCACCATC
65 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCATC
*
42493679 TTT
129 CTT
* * * *
42493682 GATCTGCCCCACTACTGCTTAGGGAGACAATATCTGAAATTTTCAATCTATTCCACTGCTGCCCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CCA
* * *
42493747 GGGAAGTAGAATTATTGGTTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT-T-CACTAT
65 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGC-C-AT
42493810 -CTT
128 CCTT
*
42493813 CGATCTGTTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCC
1 -GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CC
* * *
42493878 AGGGAAGTAGAATTGCTGGTTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGTCATC
64 AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
*
42493943 TTT
129 CTT
* * * *
42493946 GACCTGCTCCACTACTGTTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTACTGTCTA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CCA
* *
42494011 GGGAAGTAGAATTGCTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCT
65 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCC
42494076 TT
130 TT
* * *
42494078 GATCTACTCCACTACTGTTTAGGGAGACAAGATCTGAAATATTCAATCTATTCCGCTGCTGTCCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CCA
* * * * *
42494143 GGGAAGTAGAATTACTGGCTTCAATGTACTTCACTGTAACCTCGGGGAGGTAAAATCCGTCAT-C
65 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCC
42494207 TT
130 TT
*
42494209 CGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTACTGTCC
1 -GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CC
*
42494274 AGGGAAGTAGAATTGCTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
64 AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
*
42494339 TTT
129 CTT
* * *
42494342 GATCTGCTCCACTACTGTTTAGGGAGACAAGATCTGAAATATTCAATCTATTCCGCTGCTATCCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCT-GCCA
* * *
42494407 GGGAAGTAGAATTACTGGCTTCAATGT-CTTCACTGTAACCTCAGGGAGGTAAAATCCGCCAT-C
65 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCC
42494470 TT
130 TT
42494472 CGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCC
1 -GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CC
* * *
42494537 AGGAAAGTAGAATTACTGGCTTCAATGTACTCCGCTGTAACTACAGGGAGGTAAAATCTGCCATC
64 AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
*
42494602 TTT
129 CTT
*
42494605 GATATGCT
1 GATCTGCT
42494613 TCGCTGTTTA
Statistics
Matches: 955, Mismatches: 93, Indels: 30
0.89 0.09 0.03
Matches are distributed among these distances:
130 3 0.00
131 125 0.13
132 817 0.86
133 10 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (131 bp):
GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCAG
GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCCT
T
Found at i:42495996 original size:8 final size:7
Alignment explanation
Indices: 42495961--42495993 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
42495951 CTATTTTTAC
42495961 TTTTTCA
1 TTTTTCA
42495968 TTTTTCA
1 TTTTTCA
42495975 -TTTTCA
1 TTTTTCA
42495981 TCTTTTCA
1 T-TTTTCA
42495989 TTTTT
1 TTTTT
42495994 TCACATCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:42502660 original size:42 final size:42
Alignment explanation
Indices: 42502613--42502701 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
42502603 AATATGTAAT
*
42502613 TCACTAACACATCTTGCCATATACAATATCCAATTGGTGAAA
1 TCACTAACACATCTTGCCAAATACAATATCCAATTGGTGAAA
42502655 TCACTAACACATCTTGCCAAATACAATATCCAATTGGTGAAA
1 TCACTAACACATCTTGCCAAATACAATATCCAATTGGTGAAA
42502697 TCACT
1 TCACT
42502702 TAAATGAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (42 bp):
TCACTAACACATCTTGCCAAATACAATATCCAATTGGTGAAA
Found at i:42502872 original size:49 final size:48
Alignment explanation
Indices: 42502819--42502957 Score: 215
Period size: 49 Copynumber: 2.8 Consensus size: 48
42502809 CTTATTTTCT
*
42502819 CGATGTCATAGTCCAACTATGGTCTTACACGTAATCACATAACATATAC
1 CGATGTCATAG-CCAGCTATGGTCTTACACGTAATCACATAACATATAC
*
42502868 CGATGCCATAGCCTAGCTATGGTCTTACACGTAATCACATAACATATAC
1 CGATGTCATAGCC-AGCTATGGTCTTACACGTAATCACATAACATATAC
* *
42502917 CGATGTTATAGCCCAGCTATGGTCTTACACGGAATCACATA
1 CGATGTCATAG-CCAGCTATGGTCTTACACGTAATCACATA
42502958 TCACTTATTG
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
48 2 0.02
49 79 0.95
50 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (48 bp):
CGATGTCATAGCCAGCTATGGTCTTACACGTAATCACATAACATATAC
Found at i:42504169 original size:23 final size:23
Alignment explanation
Indices: 42504143--42504241 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
42504133 ATAAGTGCCA
42504143 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
42504166 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
42504189 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
42504212 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
42504235 CACTGAT
1 CACTGAT
42504242 CATTAACACT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:42505884 original size:19 final size:19
Alignment explanation
Indices: 42505815--42505887 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 19
42505805 ATTTTAAAAT
*
42505815 TTATTAAATTGAACTATAA
1 TTATTAAATTAAACTATAA
* * *
42505834 TTATTAAA-AAAATTAGAA
1 TTATTAAATTAAACTATAA
42505852 TTACATTTAAAAATTAAACTATAA
1 TT--A-TT--AAATTAAACTATAA
42505876 TTATTAAATTAA
1 TTATTAAATTAA
42505888 GTTATTCGAC
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
18 8 0.20
19 15 0.37
20 1 0.02
21 4 0.10
22 1 0.02
23 3 0.07
24 9 0.22
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (19 bp):
TTATTAAATTAAACTATAA
Found at i:42512221 original size:17 final size:17
Alignment explanation
Indices: 42512185--42512218 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42512175 ATATAAAAAG
*
42512185 TTAAATAAAAAATTAAA
1 TTAAATAAAAAAATAAA
42512202 TTAAATTAAAAAAATAA
1 TTAAA-TAAAAAAATAA
42512219 TTAGACCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAATAAAAAAATAAA
Found at i:42515870 original size:35 final size:35
Alignment explanation
Indices: 42515824--42515894 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
42515814 ACACAGATGA
42515824 CACATTATATTTTAAACAGCATCTGAAAGTTAATT
1 CACATTATATTTTAAACAGCATCTGAAAGTTAATT
*
42515859 CACATTATATTTTAAACGGCATCTGAAAGTTAATT
1 CACATTATATTTTAAACAGCATCTGAAAGTTAATT
42515894 C
1 C
42515895 TCAAAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (35 bp):
CACATTATATTTTAAACAGCATCTGAAAGTTAATT
Found at i:42519700 original size:16 final size:17
Alignment explanation
Indices: 42519679--42519711 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
42519669 TATATTTATT
42519679 TTTTAAAAT-TTTTTAA
1 TTTTAAAATATTTTTAA
42519695 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
42519712 AATACTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:42519732 original size:40 final size:40
Alignment explanation
Indices: 42519686--42519763 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
42519676 ATTTTTTAAA
42519686 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTT
1 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTT
42519726 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
1 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
42519764 AATTTTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (40 bp):
ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTT
Found at i:42520201 original size:18 final size:17
Alignment explanation
Indices: 42520178--42520220 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 17
42520168 ATATTTTTTT
42520178 ATTTAAATCAAAATCAAA
1 ATTTAAATCAAAAT-AAA
*
42520196 ATTTAAATCAAAATGAA
1 ATTTAAATCAAAATAAA
42520213 ATTTAAAT
1 ATTTAAAT
42520221 TTTATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (17 bp):
ATTTAAATCAAAATAAA
Found at i:42520264 original size:111 final size:111
Alignment explanation
Indices: 42520085--42520316 Score: 299
Period size: 111 Copynumber: 2.1 Consensus size: 111
42520075 ACAATTTTGT
* *
42520085 ATTTAAGTCAGAAAGAAATTTGAAATTTATACACTATCATGGTTATCCTGTTAAAATTTTACAAT
1 ATTTAAATCAGAAAGAAATTTGAAATTTATACACTATCATGGTTATCCAGTTAAAATTTTACAAT
* * * *
42520150 TTAAAAATAACTAAATAA-ATATTTTTTTATTTAAATCAAAATCAAA
66 TTAAAAATAACTAAATAAGAAAATTGTGTATTTAAATCAAAAT-AAA
* * * *
42520196 ATTTAAATCA-AAATGAAATTT-AAATTTTATATATTATCATTGTTATCCAGTTAAAATTTTATA
1 ATTTAAATCAGAAA-GAAATTTGAAA-TTTATACACTATCATGGTTATCCAGTTAAAATTTTACA
*
42520259 ATTTAAAAATAATTAAATAAGTAAAATTGTGTATTTAAATCAAAATAAA
64 ATTTAAAAATAACTAAATAAG-AAAATTGTGTATTTAAATCAAAATAAA
42520308 ATTTGAAAT
1 ATTT-AAAT
42520317 TTATACTAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
110 6 0.06
111 68 0.65
112 7 0.07
113 24 0.23
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (111 bp):
ATTTAAATCAGAAAGAAATTTGAAATTTATACACTATCATGGTTATCCAGTTAAAATTTTACAAT
TTAAAAATAACTAAATAAGAAAATTGTGTATTTAAATCAAAATAAA
Found at i:42520481 original size:20 final size:22
Alignment explanation
Indices: 42520433--42520488 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
42520423 TAAATTAAAC
* *
42520433 AATTTTTAAAATAAAGTTTTGA
1 AATTCTTAAAATATAGTTTTGA
*
42520455 TATTCTTAAAATATA-TTTT-A
1 AATTCTTAAAATATAGTTTTGA
42520475 AATTCTTAAAATAT
1 AATTCTTAAAATAT
42520489 TTTCTTAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 14 0.47
21 4 0.13
22 12 0.40
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (22 bp):
AATTCTTAAAATATAGTTTTGA
Found at i:42520583 original size:17 final size:17
Alignment explanation
Indices: 42520561--42520593 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42520551 ATTGATAACA
42520561 TTAAAAA-AATTTAAATT
1 TTAAAAATAA-TTAAATT
42520578 TTAAAAATAATTAAAT
1 TTAAAAATAATTAAAT
42520594 AAATAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATAATTAAATT
Found at i:42521275 original size:26 final size:27
Alignment explanation
Indices: 42521217--42521278 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
42521207 GAAAAAAATA
*
42521217 TAAATTATTATTTTAATATAATTAAAT
1 TAAATTATTATTTTAATATAATTAAAC
* *
42521244 TGAATTGTT-TTTTAATATAATTAAAC
1 TAAATTATTATTTTAATATAATTAAAC
42521270 TAAATTATT
1 TAAATTATT
42521279 GAGCTAACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 23 0.77
27 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (27 bp):
TAAATTATTATTTTAATATAATTAAAC
Found at i:42521384 original size:49 final size:48
Alignment explanation
Indices: 42521330--42521423 Score: 161
Period size: 48 Copynumber: 1.9 Consensus size: 48
42521320 AATTATTTTA
*
42521330 TTATGAGTTTATTTATTTTTGTGTCTTTTCTTGGATTAAATTAATGTAT
1 TTATGAGTTTATTTATTTTTG-CTCTTTTCTTGGATTAAATTAATGTAT
*
42521379 TTATGATTTTATTTATTTTTGCTCTTTTCTTGGATTAAATTAATG
1 TTATGAGTTTATTTATTTTTGCTCTTTTCTTGGATTAAATTAATG
42521424 CGTTTATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
48 23 0.53
49 20 0.47
ACGTcount: A:0.22, C:0.05, G:0.13, T:0.60
Consensus pattern (48 bp):
TTATGAGTTTATTTATTTTTGCTCTTTTCTTGGATTAAATTAATGTAT
Found at i:42521534 original size:26 final size:28
Alignment explanation
Indices: 42521479--42521536 Score: 84
Period size: 26 Copynumber: 2.1 Consensus size: 28
42521469 GAAAAAACTA
**
42521479 AATTATTATTTTAATATAAATTAAGTTG
1 AATTATTATTTTAATATAAATTAAAATG
42521507 AATTATT-TTTTAATAT-AATTAAAATG
1 AATTATTATTTTAATATAAATTAAAATG
42521533 AATT
1 AATT
42521537 GTTGAGCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 12 0.43
27 9 0.32
28 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (28 bp):
AATTATTATTTTAATATAAATTAAAATG
Found at i:42521642 original size:14 final size:15
Alignment explanation
Indices: 42521623--42521651 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42521613 AACGCCCTGA
42521623 TTTCGT-AATTTTAT
1 TTTCGTAAATTTTAT
42521637 TTTCGTAAATTTTAT
1 TTTCGTAAATTTTAT
42521652 CATAAATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTCGTAAATTTTAT
Found at i:42526979 original size:23 final size:23
Alignment explanation
Indices: 42526948--42526998 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
42526938 ACCTACTTTC
* * *
42526948 TTACTGTAGTAATTTTTGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
42526971 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
42526994 TTACA
1 TTACA
42526999 TTAATTGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:42527767 original size:28 final size:28
Alignment explanation
Indices: 42527735--42527790 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
42527725 TCGCCTAAGG
42527735 CTGAGGATTACCTGCACAGTTAAGAGGA
1 CTGAGGATTACCTGCACAGTTAAGAGGA
42527763 CTGAGGATTACCTGCACAGTTAAGAGGA
1 CTGAGGATTACCTGCACAGTTAAGAGGA
42527791 GAGGGTGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (28 bp):
CTGAGGATTACCTGCACAGTTAAGAGGA
Found at i:42527929 original size:28 final size:28
Alignment explanation
Indices: 42527896--42527969 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
42527886 AGTACAATGA
** *
42527896 AGGCCTTAGCCCAATTTAGTAGCAGTGT
1 AGGCCTTAGCCCAATACAATAGCAGTGT
* *
42527924 GGGCCTTAGCCCAATACAATATCAGTGT
1 AGGCCTTAGCCCAATACAATAGCAGTGT
42527952 AGGCCTTAGCCCAATACA
1 AGGCCTTAGCCCAATACA
42527970 GTAACATTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (28 bp):
AGGCCTTAGCCCAATACAATAGCAGTGT
Found at i:42528354 original size:27 final size:26
Alignment explanation
Indices: 42528324--42528763 Score: 425
Period size: 27 Copynumber: 16.4 Consensus size: 26
42528314 GGTATAAAAA
42528324 TCATTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCT-TAGGGGTATTTCGG
* * *
42528351 TCATTCTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCT-TAGGGGTATTTCGG
* * **
42528378 TCATTTTATCCTTCGGGGGTATTTCTA
1 TCATTTTACCCTT-AGGGGTATTTCGG
* *
42528405 TTATTTTACCCTTTGAGGGTA-TTCAGG
1 TCATTTTACCCTTAG-GGGTATTTC-GG
* *
42528432 TCATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTAG-GGGTATTTCGG
*
42528459 TCATTTTACCCTTCAGGGGTATTTCGA
1 TCATTTTACCCTT-AGGGGTATTTCGG
* * * *
42528486 TCATTTTACCCGTCAAGGTTATTTCGA
1 TCATTTTACCC-TTAGGGGTATTTCGG
*
42528513 TCATTTTACCCTTTGGGGTATTTCGG
1 TCATTTTACCCTTAGGGGTATTTCGG
* * *
42528539 TCATTTTACCTTTGGGGGTATTTTGG
1 TCATTTTACCCTTAGGGGTATTTCGG
**
42528565 TCATTTTACCCTTAGAGGGTATTTCAA
1 TCATTTTACCCTTAG-GGGTATTTCGG
* *
42528592 TCATTTTACCCTTTGAGGGTATTTTGG
1 TCATTTTACCCTTAG-GGGTATTTCGG
*
42528619 TCATTTTATCCTTTAGGGGTATTTCGG
1 TCATTTTA-CCCTTAGGGGTATTTCGG
* *
42528646 TCATTTTACCATTCGAGGGTATTTCGG
1 TCATTTTACCCTTAG-GGGTATTTCGG
* *
42528673 TCATTTTACCCTTTGAGGGTATTTTGG
1 TCATTTTACCCTTAG-GGGTATTTCGG
* * **
42528700 TCATTTTACCCTTCGAGTGTATTTCAT
1 TCATTTTACCCTTAG-GGGTATTTCGG
*
42528727 TCATTTTACCCTTTGGGGGTATTTCGG
1 TCATTTTACCC-TTAGGGGTATTTCGG
42528754 TCA-TTTACCC
1 TCATTTTACCC
42528764 ATAACTCGCA
Statistics
Matches: 351, Mismatches: 52, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
26 63 0.18
27 275 0.78
28 13 0.04
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (26 bp):
TCATTTTACCCTTAGGGGTATTTCGG
Found at i:42528381 original size:54 final size:54
Alignment explanation
Indices: 42528324--42528763 Score: 512
Period size: 54 Copynumber: 8.2 Consensus size: 54
42528314 GGTATAAAAA
* * * *
42528324 TCATTTTACCCTATAG-GGGTATTTCGGTCATTCTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCT-TCGAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTCGG
* * ** * *
42528378 TCATTTTATCCTTCGGGGGTATTTCTATTATTTTACCCTTTGAGGGTA-TTCAGG
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTC-GG
* ** *
42528432 TCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAGGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTCGG
* * * *
42528486 TCATTTTACCCGTCAAGGTTATTTCGATCATTTTACCCTTT-GGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTCGG
* * * * * **
42528539 TCATTTTA-CCTTTGGGGGTATTTTGGTCATTTTACCCTTAGAGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTCGG
* * * *
42528592 TCATTTTACCCTTTGAGGGTATTTTGGTCATTTTATCCTTTAGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTCGG
* * *
42528646 TCATTTTACCATTCGAGGGTATTTCGGTCATTTTACCCTTTGAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTCGG
* **
42528700 TCATTTTACCCTTCGAGTGTATTTCATTCATTTTACCCTTTGGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTCGG
42528754 TCA-TTTACCC
1 TCATTTTACCC
42528764 ATAACTCGCA
Statistics
Matches: 328, Mismatches: 53, Indels: 11
0.84 0.14 0.03
Matches are distributed among these distances:
52 24 0.07
53 48 0.15
54 253 0.77
55 3 0.01
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (54 bp):
TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTCGG
Found at i:42528434 original size:81 final size:80
Alignment explanation
Indices: 42528323--42528763 Score: 489
Period size: 81 Copynumber: 5.5 Consensus size: 80
42528313 GGGTATAAAA
* * * * *
42528323 ATCATTTTACCCTAT-AGGGGTATTTCGGTCATTCTACCCTATGGGGGTATTTCGATCATTTTAT
1 ATCATTTTACCCTTTGA-GGGTATTTCGGTCATTTTACCCT-TGAGGGTATTTCGGTCATTTTAC
*
42528387 CCTTCGGGGGTATTTCT
64 CCTTCGGGGGTATTTCG
* *
42528404 ATTATTTTACCCTTTGAGGGTA-TTCAGGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTAC
1 ATCATTTTACCCTTTGAGGGTATTTC-GGTCATTTTACCCTT-GAGGGTATTTCGGTCATTTTAC
*
42528468 CCTTCAGGGGTATTTCG
64 CCTTCGGGGGTATTTCG
* ** * *
42528485 ATCATTTTACCCGTCAAGGTTATTTCGATCATTTTACCCTTTG-GGGTATTTCGGTCATTTTA-C
1 ATCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCC-TTGAGGGTATTTCGGTCATTTTACC
* *
42528548 CTTTGGGGGTATTTTG
65 CTTCGGGGGTATTTCG
* * ** * *
42528564 GTCATTTTACCCTTAGAGGGTATTTCAATCATTTTACCCTTTGAGGGTATTTTGGTCATTTTATC
1 ATCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCC-TTGAGGGTATTTCGGTCATTTTACC
**
42528629 CTTTAGGGGTATTTCG
65 CTTCGGGGGTATTTCG
* * * *
42528645 GTCATTTTACCATTCGAGGGTATTTCGGTCATTTTACCCTTTGAGGGTATTTTGGTCATTTTACC
1 ATCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCC-TTGAGGGTATTTCGGTCATTTTACC
* *
42528710 CTTCGAGTGTATTTC-
65 CTTCGGGGGTATTTCG
*
42528725 ATTCATTTTACCCTTTGGGGGTATTTCGGTCA-TTTACCC
1 A-TCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCC
42528764 ATAACTCGCA
Statistics
Matches: 313, Mismatches: 39, Indels: 17
0.85 0.11 0.05
Matches are distributed among these distances:
79 51 0.16
80 47 0.15
81 209 0.67
82 6 0.02
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (80 bp):
ATCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCCTTGAGGGTATTTCGGTCATTTTACCC
TTCGGGGGTATTTCG
Found at i:42534220 original size:12 final size:11
Alignment explanation
Indices: 42534203--42534237 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
42534193 GCCACCCCCT
42534203 ACCACTGCGACA
1 ACCACTGC-ACA
42534215 ACCACTGCAC-
1 ACCACTGCACA
42534225 ACCACTGCACA
1 ACCACTGCACA
42534236 AC
1 AC
42534238 TCCTCTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 4 0.18
12 8 0.36
ACGTcount: A:0.34, C:0.46, G:0.11, T:0.09
Consensus pattern (11 bp):
ACCACTGCACA
Found at i:42535500 original size:15 final size:14
Alignment explanation
Indices: 42535479--42535514 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
42535469 ATAATCTTTA
42535479 ATAATTATCTCAAT
1 ATAATTATCTCAAT
*
42535493 ATTAATTATCTTAAT
1 A-TAATTATCTCAAT
42535508 ATAATTA
1 ATAATTA
42535515 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCTCAAT
Found at i:42537156 original size:10 final size:10
Alignment explanation
Indices: 42537141--42537173 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
42537131 AAGTAAAGAA
42537141 AAATAATAAT
1 AAATAATAAT
42537151 AAATAATAAT
1 AAATAATAAT
*
42537161 AAATAAAAAT
1 AAATAATAAT
42537171 AAA
1 AAA
42537174 AATTGGGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAATAATAAT
Found at i:42543647 original size:15 final size:14
Alignment explanation
Indices: 42543626--42543661 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
42543616 ATAATCTTTA
42543626 ATAATTATCTCAAT
1 ATAATTATCTCAAT
*
42543640 ATTAATTATCTTAAT
1 A-TAATTATCTCAAT
42543655 ATAATTA
1 ATAATTA
42543662 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCTCAAT
Found at i:42544613 original size:20 final size:21
Alignment explanation
Indices: 42544577--42544617 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
42544567 CTTACATGCC
*
42544577 AAAGTGAAAAAATTGATTTTT
1 AAAGTGAAAAAAGTGATTTTT
42544598 AAAGTG-AAAAAGTGATTTTT
1 AAAGTGAAAAAAGTGATTTTT
42544618 GGTCATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (21 bp):
AAAGTGAAAAAAGTGATTTTT
Found at i:42544719 original size:47 final size:47
Alignment explanation
Indices: 42544661--42544820 Score: 223
Period size: 47 Copynumber: 3.4 Consensus size: 47
42544651 AATGAGGAAG
* * *
42544661 AAGTGGAAGTTTATTTGCAAAAGTGGTGACTTGTCCACAATATTATA
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCATAATATTATA
* *
42544708 AAGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCATAATTTTATT
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCATAATATTATA
* * **
42544755 AAGTGGCAGTTCATCTACAAAAGTGGTGGTTTGTCCATAATATTATTA
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCATAATATTA-TA
42544803 AA-TGGCAGTTTATCTGCA
1 AAGTGGCAGTTTATCTGCA
42544821 TTACTGTGAC
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
47 96 0.97
48 3 0.03
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (47 bp):
AAGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCATAATATTATA
Found at i:42545992 original size:21 final size:21
Alignment explanation
Indices: 42545967--42546008 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42545957 ATACATGGTA
*
42545967 AAAGGTATTGATAATTTTTGT
1 AAAGGTATCGATAATTTTTGT
*
42545988 AAAGGTATCGATACTTTTTGT
1 AAAGGTATCGATAATTTTTGT
42546009 GTAAATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (21 bp):
AAAGGTATCGATAATTTTTGT
Found at i:42546243 original size:22 final size:24
Alignment explanation
Indices: 42546218--42546261 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
42546208 ATTTTGTTCA
42546218 ACTTTAACTT-TTAT-TCAAAAAC
1 ACTTTAACTTGTTATATCAAAAAC
*
42546240 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
42546262 GATATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAAAC
Found at i:42549979 original size:3 final size:3
Alignment explanation
Indices: 42549971--42550029 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
42549961 TTTCATTTTC
* *
42549971 TCT TCT TCT TCT TCT TCT TCT TCT TCT TAT TCT TAT TCT TCT TCT TC-
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
42550018 TCT TCT TCT TCT
1 TCT TCT TCT TCT
42550030 ATTGCCCAGG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:42550445 original size:57 final size:56
Alignment explanation
Indices: 42550290--42550455 Score: 183
Period size: 56 Copynumber: 2.9 Consensus size: 56
42550280 GTTGGGTTAG
* * * * * * *
42550290 TGGTGGAAAAGAATAAAGAAAAAAAAGTGGTGGGCCATGGTATT-ATGAAGGGCTTG
1 TGGTGGAAAAGAATAAAG-ATAAATAGTGGTGGGCGAAGGCATTAATGAAGGGCATA
* * * *
42550346 TGGTGGAAAGGAA-AAAAATAAATAAGTGGTGGGCGAATGCATTAATGAAGTGCATA
1 TGGTGGAAAAGAATAAAGATAAAT-AGTGGTGGGCGAAGGCATTAATGAAGGGCATA
*
42550402 TGGTGGAAAAGAATAATGATGAAATAGTGGTGGGCGAAGGCATTAATGAAGGGC
1 TGGTGGAAAAGAATAAAGAT-AAATAGTGGTGGGCGAAGGCATTAATGAAGGGC
42550456 CTGTTGAACG
Statistics
Matches: 90, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
54 4 0.04
55 18 0.20
56 33 0.37
57 31 0.34
58 4 0.04
ACGTcount: A:0.40, C:0.05, G:0.34, T:0.21
Consensus pattern (56 bp):
TGGTGGAAAAGAATAAAGATAAATAGTGGTGGGCGAAGGCATTAATGAAGGGCATA
Found at i:42550503 original size:30 final size:30
Alignment explanation
Indices: 42550469--42550526 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
42550459 TTGAACGGTC
*
42550469 AAATGGGTTGCTAAGAAATGAAATTGGGTT
1 AAATGGGTTACTAAGAAATGAAATTGGGTT
*
42550499 AAATGGGTTATTAAGAAATGAAATTGGG
1 AAATGGGTTACTAAGAAATGAAATTGGG
42550527 CAAGATCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.29, T:0.29
Consensus pattern (30 bp):
AAATGGGTTACTAAGAAATGAAATTGGGTT
Found at i:42551111 original size:15 final size:15
Alignment explanation
Indices: 42551091--42551120 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42551081 TTAGTGGAGA
42551091 AAAAGCAGATTCGAT
1 AAAAGCAGATTCGAT
42551106 AAAAGCAGATTCGAT
1 AAAAGCAGATTCGAT
42551121 TATCGCAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (15 bp):
AAAAGCAGATTCGAT
Found at i:42556023 original size:22 final size:22
Alignment explanation
Indices: 42555995--42556040 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
42555985 GGAAATCATT
42555995 TCCACTTCATTCAACCACTTGG
1 TCCACTTCATTCAACCACTTGG
42556017 TCCACTTCATTCAACCACTTGG
1 TCCACTTCATTCAACCACTTGG
42556039 TC
1 TC
42556041 TGAATTGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.37, G:0.09, T:0.33
Consensus pattern (22 bp):
TCCACTTCATTCAACCACTTGG
Found at i:42558506 original size:17 final size:17
Alignment explanation
Indices: 42558472--42558515 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
42558462 GAAATTATTA
* *
42558472 AAATAAGTTTTTATATT
1 AAATAAGTTATTAAATT
42558489 AAATAAGTTATTAAATT
1 AAATAAGTTATTAAATT
*
42558506 -ATTAAGTTAT
1 AAATAAGTTAT
42558516 ATTATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (17 bp):
AAATAAGTTATTAAATT
Found at i:42559600 original size:100 final size:99
Alignment explanation
Indices: 42559405--42559619 Score: 317
Period size: 102 Copynumber: 2.2 Consensus size: 99
42559395 AGAGTACGAG
****
42559405 AAAAAGT-AAAAAAAAAATTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTTAAATTTTTTTT
1 AAAAAGTAAAAAAAAAAATTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTTAAA--TAAAAT
* * *
42559469 TTACTTTTTTTGTGTTAGATAAGATATCAGTATACAA
64 TTACTTTTTTCGTGTCAAATAAGATATCAGTATAC-A
42559506 AAAAAGTAAAAAAAAAAATTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTTTAAA-AAAATT
1 AAAAAGTAAAAAAAAAAATTGGTGGTGGCCTGGCAATGGCCGGCACCACC-TTTTAAATAAAATT
42559570 TACTTTTTTCGTGTCAAATAAGATATCAGTATACA
65 TACTTTTTTCGTGTCAAATAAGATATCAGTATACA
42559605 AAAAAGTAAAAAAAA
1 AAAAAGTAAAAAAAA
42559620 TTACTTTTTT
Statistics
Matches: 105, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
99 16 0.15
100 33 0.31
101 7 0.07
102 42 0.40
103 7 0.07
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (99 bp):
AAAAAGTAAAAAAAAAAATTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTTAAATAAAATTT
ACTTTTTTCGTGTCAAATAAGATATCAGTATACA
Found at i:42559620 original size:52 final size:52
Alignment explanation
Indices: 42559560--42559671 Score: 190
Period size: 51 Copynumber: 2.2 Consensus size: 52
42559550 ACCACCTTTT
*
42559560 TAAAAAAATTTACTTTTTTCGTGTCAAATAAGATATCAGTATAC-AAAAAAG
1 TAAAAAAAATTACTTTTTTCGTGTCAAATAAGATATCAGTATACGAAAAAAG
* *
42559611 TAAAAAAAATTACTTTTTTCGTGTCAGATAAGCTATCAGTATACGAAAAAAG
1 TAAAAAAAATTACTTTTTTCGTGTCAAATAAGATATCAGTATACGAAAAAAG
42559663 TAAAAAAAA
1 TAAAAAAAA
42559672 AATTGGTGGT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 41 0.72
52 16 0.28
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (52 bp):
TAAAAAAAATTACTTTTTTCGTGTCAAATAAGATATCAGTATACGAAAAAAG
Found at i:42562319 original size:97 final size:98
Alignment explanation
Indices: 42562132--42562584 Score: 504
Period size: 97 Copynumber: 4.5 Consensus size: 98
42562122 CCTATATATA
* * * *
42562132 TTTTAAAAAAGGTGGTGTCGGCCATTGGCAGGCCACCACTAAATTTTTTTTAACTTTTTTCGTAT
1 TTTTTAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCAC-AAATTTTTTTTTACTTTTTTCGTAT
* *
42562197 ACTGATAGCTTATCTGATACGAAAAAAGTAATTT
65 ACTGATATCTTATCTGACACGAAAAAAGTAATTT
* * *
42562231 TTTTTAAAAAGGTGATGCCGGCCATTGGCAGGCCACCAC-AATTTTTTTTTACTTTTTTTGTATA
1 TTTTTAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCACAAATTTTTTTTTACTTTTTTCGTATA
* * *
42562295 CTGATACCTTATTTGACACGAAAAAAGAAATTTT
66 CTGATATCTTATCTGACACGAAAAAAGTAA-TTT
* *
42562329 TTTTTAAAAAAAGGTGGCGCTGGCCATTGCCAGGCCACCACTAAAAAAAATAATTTTTTTTTTAC
1 TTTTT--AAAAAGGTGGTGCCGGCCATTGCCAGGCCACCAC--------A-AA-TTTTTTTTTAC
* * **
42562394 TTTTTTCGTATACTGATATCTTATCTGAAACGAAAAAATTAAAAAT
54 TTTTTTCGTATACTGATATCTTATCTGACACGAAAAAAGT-AATTT
* * *
42562440 TTTTT--AAAGGTGGTGCCGGCTATTTCCAGGCCACCACGAATTTTTTTTTACTTTTTTCGTATA
1 TTTTTAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCACAAATTTTTTTTTACTTTTTTCGTATA
* *
42562503 CTAATATCTTATCTGACACGAAAAATGTAA-TT
66 CTGATATCTTATCTGACACGAAAAAAGTAATTT
*
42562535 TTTTT--AAAGGTGGTGCCGGCCATTTCCAGGCCACCACCAAATTTTTTTTT
1 TTTTTAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCA-CAAATTTTTTTTT
42562585 TTTACTTTTT
Statistics
Matches: 305, Mismatches: 33, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
95 36 0.12
96 14 0.05
97 96 0.31
98 10 0.03
99 36 0.12
100 30 0.10
107 28 0.09
110 2 0.01
111 51 0.17
112 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (98 bp):
TTTTTAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCACAAATTTTTTTTTACTTTTTTCGTATA
CTGATATCTTATCTGACACGAAAAAAGTAATTT
Found at i:42565590 original size:16 final size:16
Alignment explanation
Indices: 42565569--42565599 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42565559 CATATTAGAG
42565569 CATATAAATTTGAAAT
1 CATATAAATTTGAAAT
*
42565585 CATATATATTTGAAA
1 CATATAAATTTGAAA
42565600 ACTTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
CATATAAATTTGAAAT
Found at i:42566584 original size:21 final size:22
Alignment explanation
Indices: 42566551--42566591 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
42566541 GAGGAGTTAG
42566551 ATTTTATTTTATTTTTATTAAA
1 ATTTTATTTTATTTTTATTAAA
42566573 ATTTTA-TTTATTTTTATTA
1 ATTTTATTTTATTTTTATTA
42566592 TTAAAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTTATTTTATTTTTATTAAA
Found at i:42568219 original size:15 final size:15
Alignment explanation
Indices: 42568199--42568238 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
42568189 ACAATAGGTG
42568199 GTTCGCAT-TCAATTA
1 GTTCGCATATC-ATTA
42568214 GTTCGCATATCATTA
1 GTTCGCATATCATTA
*
42568229 GTTCACATAT
1 GTTCGCATAT
42568239 AACAAACCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 21 0.91
16 2 0.09
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (15 bp):
GTTCGCATATCATTA
Found at i:42570427 original size:8 final size:8
Alignment explanation
Indices: 42570410--42570470 Score: 70
Period size: 8 Copynumber: 7.5 Consensus size: 8
42570400 AATACATAAA
42570410 TTTT-CTT
1 TTTTCCTT
42570417 TTTTCCTT
1 TTTTCCTT
42570425 TTTTCCTT
1 TTTTCCTT
*
42570433 TTTCCCTT
1 TTTTCCTT
42570441 TCTTTCCTT
1 T-TTTCCTT
**
42570450 TTATTATTT
1 TT-TTCCTT
42570459 TTTTCCTT
1 TTTTCCTT
42570467 TTTT
1 TTTT
42570471 TTTCTTTTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
7 4 0.09
8 28 0.62
9 13 0.29
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTCCTT
Found at i:42570459 original size:25 final size:24
Alignment explanation
Indices: 42570414--42570470 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
42570404 CATAAATTTT
*
42570414 CTTTTTTCCTTTTTTCCTTTTTCC
1 CTTTTTTCCTTTTTTCATTTTTCC
*
42570438 CTTTCTTTCCTTTTATT-ATTTTTTTC
1 CTTT-TTTCCTTTT-TTCA-TTTTTCC
42570464 CTTTTTT
1 CTTTTTT
42570471 TTTCTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 4 0.14
25 12 0.43
26 12 0.43
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.74
Consensus pattern (24 bp):
CTTTTTTCCTTTTTTCATTTTTCC
Found at i:42572428 original size:13 final size:13
Alignment explanation
Indices: 42572398--42572445 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
42572388 GTTGAGGAAA
* *
42572398 TAATTTAATTAAG
1 TAATTAAATTAAT
* *
42572411 AAATTAATTTAAT
1 TAATTAAATTAAT
42572424 TAATTAAATTAAT
1 TAATTAAATTAAT
*
42572437 TGATTAAAT
1 TAATTAAAT
42572446 AAATAATCTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:42586867 original size:43 final size:43
Alignment explanation
Indices: 42586806--42586929 Score: 153
Period size: 43 Copynumber: 2.9 Consensus size: 43
42586796 ATTTCTGAAA
*
42586806 TGTGTTTTCATGTAAGACCACGTCTGGGATGTTGGCATCGACT
1 TGTGTTTACATGTAAGACCACGTCTGGGATGTTGGCATCGACT
* * *
42586849 TGTGTTTACGTGTAAGACC-CTGTCTGGGATAG-TGGCGTCGATT
1 TGTGTTTACATGTAAGACCAC-GTCTGGGAT-GTTGGCATCGACT
* * *
42586892 TGTGATCACATGTAAGACCACGTTTGGGATGTTGGCAT
1 TGTGTTTACATGTAAGACCACGTCTGGGATGTTGGCAT
42586930 TGTACGAGCT
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
42 2 0.03
43 64 0.94
44 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (43 bp):
TGTGTTTACATGTAAGACCACGTCTGGGATGTTGGCATCGACT
Found at i:42604666 original size:37 final size:38
Alignment explanation
Indices: 42604568--42604659 Score: 141
Period size: 37 Copynumber: 2.4 Consensus size: 38
42604558 ATCACATAGC
*
42604568 ACGCCACACAGGCTTCACCGAATACGCCATTACAGAAT
1 ACGCCACACAGGCTTCACCAAATACGCCATTACAGAAT
* * *
42604606 ATGCCATACGGGCTTCACCAAATACG-CATTACAGAAT
1 ACGCCACACAGGCTTCACCAAATACGCCATTACAGAAT
42604643 ACGCCACACAGGCTTCA
1 ACGCCACACAGGCTTCA
42604660 GTAAATATAC
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 25 0.53
38 22 0.47
ACGTcount: A:0.34, C:0.33, G:0.16, T:0.17
Consensus pattern (38 bp):
ACGCCACACAGGCTTCACCAAATACGCCATTACAGAAT
Found at i:42606296 original size:26 final size:26
Alignment explanation
Indices: 42606266--42606336 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 26
42606256 GAATTTTTTT
42606266 AAAATTTTATTGGGGGTAAAATCGTC
1 AAAATTTTATTGGGGGTAAAATCGTC
* *
42606292 AAAATTTTATCGGGGGTAAAATTGTC
1 AAAATTTTATTGGGGGTAAAATCGTC
*
42606318 AAAATTTTACT-GGGGTAAA
1 AAAATTTTATTGGGGGTAAA
42606337 TTTGGGGTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 8 0.20
26 33 0.80
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.34
Consensus pattern (26 bp):
AAAATTTTATTGGGGGTAAAATCGTC
Found at i:42623870 original size:18 final size:19
Alignment explanation
Indices: 42623835--42623870 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42623825 TCAAACTACA
*
42623835 AAAAAAAATCATTTTTTAG
1 AAAAAAAATCATTATTTAG
42623854 AAAAAAAAT-ATTATTTA
1 AAAAAAAATCATTATTTA
42623871 TCATTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (19 bp):
AAAAAAAATCATTATTTAG
Found at i:42632674 original size:23 final size:22
Alignment explanation
Indices: 42632623--42632674 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
42632613 CCTCGTCTTT
*
42632623 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
42632645 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
42632668 TTCTTTT
1 TTCTTTT
42632675 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:42632689 original size:18 final size:18
Alignment explanation
Indices: 42632668--42632706 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
42632658 TTTCTTCAAC
* *
42632668 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
42632686 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
42632704 TTC
1 TTC
42632707 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:42642974 original size:9 final size:9
Alignment explanation
Indices: 42642960--42643033 Score: 105
Period size: 9 Copynumber: 8.3 Consensus size: 9
42642950 TTTTGGTTAA
*
42642960 GAATTACCC
1 GAATTAACC
*
42642969 GAATTACCC
1 GAATTAACC
*
42642978 GAATTACCC
1 GAATTAACC
42642987 GAATTAACC
1 GAATTAACC
*
42642996 AAATTAACC
1 GAATTAACC
42643005 GAATTAACC
1 GAATTAACC
42643014 GAATTAACC
1 GAATTAACC
42643023 GAATT-ACC
1 GAATTAACC
42643031 GAA
1 GAA
42643034 AAATACCCGA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
8 6 0.10
9 56 0.90
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22
Consensus pattern (9 bp):
GAATTAACC
Found at i:42643729 original size:7 final size:7
Alignment explanation
Indices: 42643717--42643741 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42643707 TAGTCGATTC
42643717 GTATTTA
1 GTATTTA
42643724 GTATTTA
1 GTATTTA
42643731 GTATTTA
1 GTATTTA
42643738 GTAT
1 GTAT
42643742 ATAACTAATA
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:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTTA
Found at i:42646196 original size:127 final size:127
Alignment explanation
Indices: 42646044--42646462 Score: 675
Period size: 125 Copynumber: 3.3 Consensus size: 127
42646034 GCCAAATAGG
*
42646044 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGTTGACATTGCATCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACATTGCATCC
* *
42646109 TGCTTGAAGCATTTTTGACATTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTTCAGA
* * * *
42646171 AACTACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTCTTTCAGTACTTTTGCTAACATTGCTTCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACATTGCATCC
*
42646236 TGCTTGAAGCGTTTTTGACACTATTTTCTCAGAAACATCTTCTCAAAA-T-TTTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTTCAGA
* * * *
42646296 AACAACTGTAGTAAAACAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACAATGCATCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACATTGCATCC
* *
42646361 TGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTA-TTTTTTCAGG
66 TGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTTCAGA
*
42646422 AACTATTGTAGCAAAAGAGCGTCCACGTGGGAGCTT-TTTTA
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTA
42646463 AATTAACAAA
Statistics
Matches: 267, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
125 119 0.45
126 43 0.16
127 105 0.39
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (127 bp):
AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACATTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTTCAGA
Found at i:42646706 original size:99 final size:97
Alignment explanation
Indices: 42646501--42646934 Score: 498
Period size: 97 Copynumber: 4.4 Consensus size: 97
42646491 CTAAACCCTA
* * * *
42646501 AACCTTAAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCAAAACCCAAAACACTAAATCCTA
1 AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCTAAACCCTAAACCCT-AAT-C--
** * *
42646565 ATATATATTTTTTTAAATTTATAATTAATTTACTCAAAT
62 -TA-AT-TTTTTAAAAATTTATAATTAATTTATTCAAGT
* * * *
42646604 AACCCCAAACCCTAATTTATTTGATTTTTTCTTTAAAAATCCTAAACACTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCTAAACCCTAAACCCTAATCTAA-
42646669 TTTTTTTAAAAATTTATAATTAATTTATTCAAGT
65 -TTTTTTAAAAATTTATAATTAATTTATTCAAGT
* *
42646703 AACCCTAAACCCTAATTTATTTGATTTTTTTCTTAAAAACCCTAAACCCTAAACTCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCTAAACCCTAAACCCTAATCTAAT
42646768 TTTTTAAAAATTTATAATTAATTT-TCTCAAGT
66 TTTTTAAAAATTTATAATTAATTTAT-TCAAGT
* * * ** *
42646800 AACCTTAAACCCTAATTTATTTCATTTTTTCCTTAAAAACCATAAATGCTAAACCTTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCTAAACCCTAAACCCTAATCTAAT
** * *
42646865 TTTTTAAAAATTTATAATTAACCTAAACTCTA--
66 TTTTTAAAAATTTATAATTAA--TTTATTCAAGT
* *
42646897 AACCCTAAACCCTTATTTATTTAATTTTTTCCTTAAAA
1 AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAA
42646935 CCTTAAAATC
Statistics
Matches: 291, Mismatches: 33, Indels: 20
0.85 0.10 0.06
Matches are distributed among these distances:
96 1 0.00
97 144 0.49
98 1 0.00
99 92 0.32
100 1 0.00
102 1 0.00
103 25 0.09
104 26 0.09
ACGTcount: A:0.39, C:0.18, G:0.01, T:0.41
Consensus pattern (97 bp):
AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCTAAACCCTAAACCCTAATCTAAT
TTTTTAAAAATTTATAATTAATTTATTCAAGT
Found at i:42646854 original size:196 final size:198
Alignment explanation
Indices: 42646491--42646934 Score: 544
Period size: 196 Copynumber: 2.2 Consensus size: 198
42646481 TTAAGTAACC
* * *
42646491 CTAAACCCTAAACCTTAAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCAAAACCCAAAACA
1 CTAAACTCAAAACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCAAAACCCAAAACA
**
42646555 CTAAATCCTAATATATATTTTTTTAAATTTATAATTAATTTACTCAAATAACCCCAAACCCTAAT
66 CTAAATCC--ATATATATTTTTAAAAATTTATAATTAATTTACTCAAATAACCCCAAACCCTAAT
* *
42646620 TTATTTGATTTTTTCTTTAAAAATCCTAAACACTAAACCCTAATCTAATTTTTTTTAAAAATTTA
129 TTATTTCATTTTTTCCTTAAAAATCCTAAACACTAAACCCTAATCTAA--TTTTTTAAAAATTTA
42646685 TAATTAA
192 TAATTAA
** * * * *
42646692 -TTTATTCAAGTAACCCTAAACCCTAATTTATTTGATTTTTTTCTTAAAAACCCTAAACCCTAAA
1 CTAAACTCAA--AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCAAAACCCAAAA
* * * **
42646756 CTCT-AAT-C-TA-AT-TTTTTAAAAATTTATAATTAATTTTCTCAAGTAACCTTAAACCCTAAT
64 CACTAAATCCATATATATTTTTAAAAATTTATAATTAATTTACTCAAATAACCCCAAACCCTAAT
** *
42646816 TTATTTCATTTTTTCCTTAAAAA-CCATAAATGCTAAACCTTAATCTAATTTTTTAAAAATTTAT
129 TTATTTCATTTTTTCCTTAAAAATCC-TAAACACTAAACCCTAATCTAATTTTTTAAAAATTTAT
42646880 AATTAA
193 AATTAA
* * *
42646886 CCTAAACTCTAAACCCTAAACCCTTATTTATTTAATTTTTTCCTTAAAA
1 -CTAAACTCAAAACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAA
42646935 CCTTAAAATC
Statistics
Matches: 209, Mismatches: 28, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
194 57 0.27
195 2 0.01
196 87 0.42
197 2 0.01
198 2 0.01
200 4 0.02
201 1 0.00
202 26 0.12
203 28 0.13
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.41
Consensus pattern (198 bp):
CTAAACTCAAAACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCAAAACCCAAAACA
CTAAATCCATATATATTTTTAAAAATTTATAATTAATTTACTCAAATAACCCCAAACCCTAATTT
ATTTCATTTTTTCCTTAAAAATCCTAAACACTAAACCCTAATCTAATTTTTTAAAAATTTATAAT
TAA
Found at i:42647537 original size:11 final size:11
Alignment explanation
Indices: 42647511--42647578 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 11
42647501 CCTCTCTCGT
42647511 AATTCCTCTC-
1 AATTCCTCTCA
42647521 AATTCCTCTCA
1 AATTCCTCTCA
42647532 AATTCCT-TCCAA
1 AATTCCTCT-C-A
42647544 AATT-CTCTCA
1 AATTCCTCTCA
*
42647554 AATTTCT-TCCAA
1 AATTCCTCT-C-A
42647566 AATT-CTCTCA
1 AATTCCTCTCA
42647576 AAT
1 AAT
42647579 CTATATTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
10 21 0.42
11 17 0.34
12 12 0.24
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (11 bp):
AATTCCTCTCA
Found at i:42647551 original size:22 final size:22
Alignment explanation
Indices: 42647521--42647578 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
42647511 AATTCCTCTC
42647521 AATTCCTCTCAAATTCCTTCCAA
1 AATT-CTCTCAAATTCCTTCCAA
*
42647544 AATTCTCTCAAATTTCTTCCAA
1 AATTCTCTCAAATTCCTTCCAA
42647566 AATTCTCTCAAAT
1 AATTCTCTCAAAT
42647579 CTATATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 30 0.88
23 4 0.12
ACGTcount: A:0.33, C:0.29, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTCTCTCAAATTCCTTCCAA
Found at i:42647661 original size:51 final size:51
Alignment explanation
Indices: 42647548--42647663 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
42647538 TTCCAAAATT
* * *
42647548 CTCTCAAATTT-CTTCCAAAATTCTCTCAAATCTATATTTAATTTTAATTTC
1 CTCTC-AATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTAAATTTC
42647599 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTAAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTAAATTTC
*
42647650 TTCTCAATTTCCTT
1 CTCTCAATTTCCTT
42647664 TTTTAAAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 5 0.08
51 55 0.92
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (51 bp):
CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTAAATTTC
Found at i:42649099 original size:23 final size:23
Alignment explanation
Indices: 42649041--42649109 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
42649031 TCCAGTGGAT
42649041 CCTAATTTAATTAAAAGCCCTAAA
1 CCTAATTTAATTAAAAGCCCT-AA
* *
42649065 CC---CTTAAATAAAAGCCCTAA
1 CCTAATTTAATTAAAAGCCCTAA
*
42649085 CCTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAAAGCCCTAA
42649108 CC
1 CC
42649110 CTAACCTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 4 0.11
21 14 0.38
23 17 0.46
24 2 0.05
ACGTcount: A:0.45, C:0.26, G:0.03, T:0.26
Consensus pattern (23 bp):
CCTAATTTAATTAAAAGCCCTAA
Found at i:42649119 original size:24 final size:23
Alignment explanation
Indices: 42649073--42649120 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
42649063 AACCCTTAAA
* **
42649073 TAAAAGCCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAACCTAAT
42649096 TAAAAACCCTAACCCTAACCTAAT
1 TAAAAACCCTAA-CCTAACCTAAT
42649120 T
1 T
42649121 CATTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.27
Consensus pattern (23 bp):
TAAAAACCCTAACCTAACCTAAT
Found at i:42651785 original size:125 final size:124
Alignment explanation
Indices: 42651486--42651853 Score: 436
Period size: 125 Copynumber: 3.0 Consensus size: 124
42651476 CCCAAACATA
* * * * *
42651486 CTACTGTAGAAAAATCGCGTCCACAAGGGCGCGATTTCACAAATTCTTCCCAAATAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *** *
42651551 TATAAGCGATTTTATATTATTTACAT-AGAAACGTCAAAAAAAATTATAGATTAAAAGAC
66 TAAAAGCGATTTTATATTATTTAC-TCAGAAACGTCAAAAAAAATTATTTCTTCAAAGAC
* * * * * *
42651610 CTACTGTAGCAAAAGCGC-ACTGATGAGGCCGCAATTTCACAAATTGTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* * * ***
42651674 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCTTCTGTGAC
65 CTAAAAGCGATTTTATATTATTTACTCAGAAACGTCAAAAAA-AATTATTTCTTCAAAGAC
*
42651735 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* **
42651800 TAAAAGTGATTTTATATTATTTTA-TCAGAAACGTCAACTCAAAATTATTTCTTC
66 TAAAAGCGATTTTATATTA-TTTACTCAGAAACGTCAA-AAAAAATTATTTCTTC
42651854 CAGGACCTTA
Statistics
Matches: 204, Mismatches: 34, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
123 2 0.01
124 88 0.43
125 108 0.53
126 6 0.03
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAAAAGCGATTTTATATTATTTACTCAGAAACGTCAAAAAAAATTATTTCTTCAAAGAC
Found at i:42654938 original size:22 final size:22
Alignment explanation
Indices: 42654889--42654953 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
42654879 GCTTAATATT
42654889 ATTTTAAATTTA-T-TATTAAC
1 ATTTTAAATTTATTGTATTAAC
*
42654909 ATTGTTTAAATTTATTGTATTACC
1 A-T-TTTAAATTTATTGTATTAAC
*
42654933 ATTTTAATTTTATATGTATTA
1 ATTTTAAATTTAT-TGTATTA
42654954 TTTTTCTAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 20 0.53
23 9 0.24
24 7 0.18
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (22 bp):
ATTTTAAATTTATTGTATTAAC
Found at i:42655148 original size:18 final size:17
Alignment explanation
Indices: 42655125--42655168 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
42655115 TTATGTAGTA
42655125 TTTATTTTTAACTATATT
1 TTTATTTTTAA-TATATT
* *
42655143 TTTATTTATTTATTTATT
1 TTTATTT-TTAATATATT
42655161 TTTATTTT
1 TTTATTTT
42655169 CCAAATTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 19 0.83
19 3 0.13
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTTTTAATATATT
Found at i:42658713 original size:24 final size:24
Alignment explanation
Indices: 42658694--42658739 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
42658684 ATTTTTGAGC
42658694 CAATT-TTCATTCATTCTTTTCGAA
1 CAATTATTCATTCATTCTTTT-GAA
* *
42658718 TAATTATTCTTTCATTCTTTTG
1 CAATTATTCATTCATTCTTTTG
42658740 GATTTTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.22, C:0.17, G:0.04, T:0.57
Consensus pattern (24 bp):
CAATTATTCATTCATTCTTTTGAA
Found at i:42659571 original size:13 final size:13
Alignment explanation
Indices: 42659549--42659591 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
42659539 TCAAGAAATC
*
42659549 AAAATCAAAAAAG
1 AAAATGAAAAAAG
42659562 AAAATGAAAAAAG
1 AAAATGAAAAAAG
* *
42659575 AAAAAGAACAAA-
1 AAAATGAAAAAAG
42659587 AAAAT
1 AAAAT
42659592 AACAAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 4 0.15
13 22 0.85
ACGTcount: A:0.79, C:0.05, G:0.09, T:0.07
Consensus pattern (13 bp):
AAAATGAAAAAAG
Found at i:42661890 original size:45 final size:45
Alignment explanation
Indices: 42661830--42661960 Score: 192
Period size: 45 Copynumber: 2.9 Consensus size: 45
42661820 GAAATAGGTT
* *
42661830 GAAGATAGCAGATCTTGTCTTTCTGTATTGGCAGCAAAGTAGATC
1 GAAGATAGCAAATCTTGTCTTTCTGTATTGGCAGCGAAGTAGATC
*
42661875 GAAGTTAGCAAATCTTGTC-TTCTTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAAATCTTGTCTTTC-TGTATTGGCAGCGAAGTAGATC
** *
42661920 GAAGATATAAAATCTTGTCTTCCTGTATTGGCAGCGAAGTA
1 GAAGATAGCAAATCTTGTCTTTCTGTATTGGCAGCGAAGTA
42661961 AATTGAGGTC
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
44 3 0.04
45 72 0.94
46 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (45 bp):
GAAGATAGCAAATCTTGTCTTTCTGTATTGGCAGCGAAGTAGATC
Found at i:42662073 original size:88 final size:87
Alignment explanation
Indices: 42661799--42662101 Score: 259
Period size: 88 Copynumber: 3.4 Consensus size: 87
42661789 ACCACAAAGC
* *
42661799 CTTATCTCCCTGAGCAGCAGTGAAATAGGTTGAAGATAGCAGATCTTGTCTTTCTGTATTGGCAG
1 CTTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAG
* * * * *
42661864 CAAAGTAGATCGAAGTTAGCAAAT
66 CGAAGTAGATCGAA--AACCACAG
* * * *** * * * ** *
42661888 CTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGATATAAAATCTTGTCTTCCTGTATTGGCA
1 CTTATCTCCCTG-AGCAGCAGTGAAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCA
* * ***
42661953 GCGAAGTAAATTG-AGGTCACAAG
65 GCGAAGTAGATCGAAAACCAC-AG
* * * *
42661976 CCTTGTCTCCCTGAGCAGCAATGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCA
1 -CTTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCA
42662041 GCGAAGTAGATCGAAAACCACAG
65 GCGAAGTAGATCGAAAACCACAG
* *
42662064 CTTTATCTCCCTAAGCAGTAGT-AGAGTAGGTTGAAGAT
1 C-TTATCTCCCTGAGCAGCAGTGA-AGTAGGTTGAAGAT
42662102 TGTAGATCCT
Statistics
Matches: 161, Mismatches: 47, Indels: 13
0.73 0.21 0.06
Matches are distributed among these distances:
87 3 0.02
88 83 0.52
89 24 0.15
90 51 0.32
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (87 bp):
CTTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAG
CGAAGTAGATCGAAAACCACAG
Found at i:42662162 original size:132 final size:129
Alignment explanation
Indices: 42662065--42662666 Score: 781
Period size: 132 Copynumber: 4.6 Consensus size: 129
42662055 AAACCACAGC
* * *
42662065 TTTATCTCCCTAAGCAGTAGTAGAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGT
1 TTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGT
* *
42662130 GGAGCAGATCAAAAACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGGTTTAAGCCACCA
66 GGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAA-TTAGTAGGGAAGCA-GTTTAAGCCACCA
42662195 G
129 G
* * *
42662196 TCCTATCTCCCTTACCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAG
1 T-TTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAG
*
42662261 TGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAATGTAGTAGGGAAGCATGTTTAAGCTACC
65 TGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAT-TAGTAGGGAAGCA-GTTTAAGCCACC
42662326 AG
128 AG
* * * *
42662328 TTTTGTCTCCCTGAGCAACAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTTCCTAAGCAGTAG
1 -TTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAG
*
42662393 TGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACC
65 TGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAA-TTAGTAGGGAAGCAG-TTTAAGCCACC
*
42662458 AA
128 AG
* * * * * * * *
42662460 TCCTATCTCCCTAAACAGCAATGGAGTAGGTTGAAGAATGCAGATCCCGTATCCCTAAGCAATAG
1 T-TTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAG
* * * * *
42662525 TGGAGCAGATCAAAGACGGTGAATTTTATATTCCCAAGGTAGTAGGGAATCAGATTTAAACCACC
65 TGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAA-TTAGTAGGGAAGCAG-TTTAAGCCACC
*
42662590 AA
128 AG
* ** * *
42662592 TCCTATCTCCCTAAGCAATAGTGGAGTAAGTTGAAGATTGTAGATCATGTCTCCCTAAGCAGTAG
1 T-TTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAG
*
42662657 TGGAGAAGAT
65 TGGAGCAGAT
42662667 AGAAGGCAGC
Statistics
Matches: 418, Mismatches: 47, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
131 3 0.01
132 414 0.99
133 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (129 bp):
TTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGT
GGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAATTAGTAGGGAAGCAGTTTAAGCCACCAG
Done.