Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold45
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: 1930935
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 50924 characters in sequence are not A, C, G, or T
File 5 of 7
Found at i:1224295 original size:51 final size:48
Alignment explanation
Indices: 1224228--1224570 Score: 301
Period size: 51 Copynumber: 6.8 Consensus size: 48
1224218 CAATGGTAAC
* * * * *
1224228 CGGTTCACATAGTAGCCTGCACGTAGTACTACACATGTGA-CAATTTCCAT
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAATTT---T
* * *
1224278 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATTAAATTTT
1 -CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGA-TCAATTTT
* *
1224328 ACGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTT
1 -CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAA-TTTT
* * *
1224378 ACGGTTCACGTAGTAGCCTTTACATAGTACTACACACGTGACCATCATTTAT
1 -CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGATCA--ATTT-T
* * * * *
1224430 CAGTACAAGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AA--TTTT
* * * * *
1224481 CGGTACACATAGTAGCCTTCACTTAGTACTGCACATGTGACCATTATTTAT
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGATCA--ATTT-T
* *
1224532 CGGTACACATAGTAGCCTTCACACAGTACTACACACGTG
1 CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTG
1224571 TTTATCGATA
Statistics
Matches: 249, Mismatches: 31, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
49 3 0.01
50 88 0.35
51 147 0.59
52 6 0.02
53 5 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (48 bp):
CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAATTTT
Found at i:1224531 original size:102 final size:102
Alignment explanation
Indices: 1224233--1224570 Score: 343
Period size: 102 Copynumber: 3.3 Consensus size: 102
1224223 GTAACCGGTT
* ** * * * * *
1224233 CACA-TAGTAGCCTGCACGTAGTACTACACATGTGA-CAATTTCCATCCGATACACGTAGTAGCC
1 CACAGTAGTAGCCTTCACACAGTACTACACACGTGACCAAGTT-C-TACGGTACACATAGTAGCC
* ** * *
1224296 TGCACATAGTACTACACACGTGATTA-AATTT-T-ACGATT
64 TTCACATAGTACTACACACGTGACCATCATTTATCA-G-TA
* * * * *
1224334 CAC-GTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTTCACGTAGTAGCCTT
1 CACAGTAGTAGCCTTCACACAGTACTACACACGTGACCAAGTTCTACGGTACACATAGTAGCCTT
*
1224398 TACATAGTACTACACACGTGACCATCATTTATCAGTA
66 CACATAGTACTACACACGTGACCATCATTTATCAGTA
1224435 CA-AGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGGTACACATAGTAGCC
1 CACAGTAGTAGCCTTCACACAGTACTACACACGTGACC-AAG-TTCTACGGTACACATAGTAGCC
* * * * *
1224498 TTCACTTAGTACTGCACATGTGACCATTATTTATCGGTA
64 TTCACATAGTACTACACACGTGACCATCATTTATCAGTA
1224537 CACA-TAGTAGCCTTCACACAGTACTACACACGTG
1 CACAGTAGTAGCCTTCACACAGTACTACACACGTG
1224571 TTTATCGATA
Statistics
Matches: 203, Mismatches: 25, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
100 38 0.19
101 70 0.34
102 90 0.44
103 5 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (102 bp):
CACAGTAGTAGCCTTCACACAGTACTACACACGTGACCAAGTTCTACGGTACACATAGTAGCCTT
CACATAGTACTACACACGTGACCATCATTTATCAGTA
Found at i:1227219 original size:11 final size:13
Alignment explanation
Indices: 1227199--1227230 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1227189 AATAAATTAA
1227199 TAAAATATCAT-T
1 TAAAATATCATAT
1227211 TAAAA-ATCATAT
1 TAAAATATCATAT
1227223 TAAAATAT
1 TAAAATAT
1227231 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:1250835 original size:24 final size:24
Alignment explanation
Indices: 1250808--1250859 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1250798 TCAAGAGGAG
* *
1250808 GATCTAGAGGAAGACTTTGAAGAA
1 GATCTAGAGGAAGACCTAGAAGAA
* *
1250832 GATCTGGAGGATGACCTAGAAGAA
1 GATCTAGAGGAAGACCTAGAAGAA
1250856 GATC
1 GATC
1250860 CTAAAGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.31, T:0.19
Consensus pattern (24 bp):
GATCTAGAGGAAGACCTAGAAGAA
Found at i:1254285 original size:135 final size:138
Alignment explanation
Indices: 1254039--1254302 Score: 345
Period size: 135 Copynumber: 1.9 Consensus size: 138
1254029 ATAGGCCTAT
* * * *
1254039 TCACACAAGCTGACGGTCGGAATGTAAGCTACACGATGCTGCTCACACAAGTTTATGAGTATCCA
1 TCACACAAGCTGAAGGTCGGAATGTAAGCTACACAATGCTGCTCACACAAGTTGACGAGTATCCA
* * * * ** * * * **
1254104 TAGCTAATGCTAGACCTTAGCCGTCGGTAGGACATTCAGGACCAGCACCTGAAACATGGTAACCT
66 CAACTAATGCTAGAACTCAAACATCAGTAGGACATTCAGGAACAGCACCCAAAACATGGTAACCT
1254169 GGGACTGC
131 GGGACTGC
* *
1254177 TCACACAAGCTGAAGGTCGGAATGT-AGCTACACAATGCTG-T-ACATAAGTTGACGAGTATCCG
1 TCACACAAGCTGAAGGTCGGAATGTAAGCTACACAATGCTGCTCACACAAGTTGACGAGTATCCA
*
1254239 CAACTAATGCTGGAACTCAAACATCAGTAGGACATTCAGGAACAGCACCCAAAACATGGTAACC
66 CAACTAATGCTAGAACTCAAACATCAGTAGGACATTCAGGAACAGCACCCAAAACATGGTAACC
1254303 CTAATGACAT
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
135 69 0.64
136 1 0.01
137 14 0.13
138 24 0.22
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (138 bp):
TCACACAAGCTGAAGGTCGGAATGTAAGCTACACAATGCTGCTCACACAAGTTGACGAGTATCCA
CAACTAATGCTAGAACTCAAACATCAGTAGGACATTCAGGAACAGCACCCAAAACATGGTAACCT
GGGACTGC
Found at i:1255847 original size:12 final size:12
Alignment explanation
Indices: 1255816--1255840 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1255806 TCGTCTCGAT
1255816 TCAAAACTCATA
1 TCAAAACTCATA
1255828 TCAAAACTCATA
1 TCAAAACTCATA
1255840 T
1 T
1255841 TAGAACTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (12 bp):
TCAAAACTCATA
Found at i:1257026 original size:15 final size:15
Alignment explanation
Indices: 1256994--1257032 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
1256984 AACAATAAGA
1256994 AAGATAAT-AAAACC
1 AAGATAATGAAAACC
*
1257008 AAGATAATGAAATCC
1 AAGATAATGAAAACC
1257023 AAGAT-ATGAA
1 AAGATAATGAA
1257033 GCTCTACTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (15 bp):
AAGATAATGAAAACC
Found at i:1260666 original size:28 final size:29
Alignment explanation
Indices: 1260634--1260695 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
1260624 TGGCCCTATT
* *
1260634 CAATAACAGT-ACAGTGTGGGCCTTAGCC
1 CAATAACAGTAACAATGTAGGCCTTAGCC
*
1260662 CAAT-ACAGTAATAATGTAGGCCTTAGCC
1 CAATAACAGTAACAATGTAGGCCTTAGCC
1260690 CAATAA
1 CAATAA
1260696 AATATCAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.17
28 23 0.79
29 1 0.03
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (29 bp):
CAATAACAGTAACAATGTAGGCCTTAGCC
Found at i:1260852 original size:26 final size:26
Alignment explanation
Indices: 1260812--1260861 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1260802 ACCAATATCG
* * *
1260812 CAACAAGGCTGCCAGTAATAGTATTA
1 CAACAAAGCTACCAGTAACAGTATTA
1260838 CAACAAAGCTACCAGTAACAGTAT
1 CAACAAAGCTACCAGTAACAGTAT
1260862 CGTAGGAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (26 bp):
CAACAAAGCTACCAGTAACAGTATTA
Found at i:1268614 original size:28 final size:27
Alignment explanation
Indices: 1268582--1268661 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
1268572 CTACCTCTAG
*
1268582 GGGTATAATGGTCATTTCTATCTATTAA
1 GGGTATAATGGTCATTT-TAACTATTAA
* **
1268610 GGGTAAAACAGTCATTTTACACT-TTAA
1 GGGTATAATGGTCATTTTA-ACTATTAA
** *
1268637 GGGTATTTTGGTCATTTTACCTATT
1 GGGTATAATGGTCATTTTAACTATT
1268662 TTGGGGTCTT
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
26 2 0.05
27 22 0.55
28 16 0.40
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (27 bp):
GGGTATAATGGTCATTTTAACTATTAA
Found at i:1277066 original size:4 final size:4
Alignment explanation
Indices: 1277057--1277082 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1277047 TGCTTCTTCT
1277057 TTAC TTAC TTAC TTAC TTAC TTAC TT
1 TTAC TTAC TTAC TTAC TTAC TTAC TT
1277083 GTTTACCCTA
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:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAC
Found at i:1278594 original size:26 final size:26
Alignment explanation
Indices: 1278565--1278633 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
1278555 TATATATAGT
*
1278565 TGCTTACACGAGCTGTGAAATAGGTA
1 TGCTTACACAAGCTGTGAAATAGGTA
* * *
1278591 TGCTCACACAAGCTGTGAAATGGGTT
1 TGCTTACACAAGCTGTGAAATAGGTA
*
1278617 TGCTTACACAAGTTGTG
1 TGCTTACACAAGCTGTG
1278634 GGTCAGAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (26 bp):
TGCTTACACAAGCTGTGAAATAGGTA
Found at i:1283654 original size:24 final size:24
Alignment explanation
Indices: 1283627--1283673 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1283617 AAATGATTGA
*
1283627 TTTGTCTGTGATTGGTATGACTGC
1 TTTGTCTGTGATTGGTATCACTGC
*
1283651 TTTGTCTGTGATTTGTATCACTG
1 TTTGTCTGTGATTGGTATCACTG
1283674 ATTCTGAGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.49
Consensus pattern (24 bp):
TTTGTCTGTGATTGGTATCACTGC
Found at i:1283856 original size:32 final size:32
Alignment explanation
Indices: 1283815--1284017 Score: 248
Period size: 32 Copynumber: 6.4 Consensus size: 32
1283805 GCTGCAATGC
* *
1283815 TACTGATGGCTTTGTGCCGATCATTTTATCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
1283847 TACTGATGGCTTTGTGCCGATCATTTTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
1283879 TTCTGATGGCTTTGTGCCTATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
1283911 TACTGATGGCTTTGTGCATG-TCATATTATCGT
1 TACTGATGGCTTTGTGC-CGATCATATTACCGT
* * * *
1283943 TACTGATGGCTGTGTGCCAATCATATCACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
1283975 TACTGATGGCTTTGTTCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
1284006 TACTTATGGCTT
1 TACTGATGGCTT
1284018 GTAGCCATTT
Statistics
Matches: 151, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
31 11 0.07
32 140 0.93
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:1283981 original size:96 final size:95
Alignment explanation
Indices: 1283815--1284017 Score: 273
Period size: 96 Copynumber: 2.1 Consensus size: 95
1283805 GCTGCAATGC
* * * * *
1283815 TACTGATGGCTTTGTGCCGATCATTTTATCGTTACTGATGGCTTTGTGCCGATCATTTTACCGTT
1 TACTGATGGCTTTGTGCCGATCATATTATCGTTACTGATGGCTGTGTGCCAATCATATCACCGTT
* *
1283880 TCTGATGGCTTTGTGCCTATCATATTACCG
66 ACTGATGGCTTTGTGCCAATCATATTACCG
* *
1283910 TTACTGATGGCTTTGTGCATG-TCATATTATCGTTACTGATGGCTGTGTGCCAATCATATCACTG
1 -TACTGATGGCTTTGTGC-CGATCATATTATCGTTACTGATGGCTGTGTGCCAATCATATCACCG
* *
1283974 TTACTGATGGCTTTGTTCCAATCATATTACTG
64 TTACTGATGGCTTTGTGCCAATCATATTACCG
*
1284006 TACTTATGGCTT
1 TACTGATGGCTT
1284018 GTAGCCATTT
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
95 11 0.12
96 82 0.87
97 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (95 bp):
TACTGATGGCTTTGTGCCGATCATATTATCGTTACTGATGGCTGTGTGCCAATCATATCACCGTT
ACTGATGGCTTTGTGCCAATCATATTACCG
Found at i:1293370 original size:6 final size:6
Alignment explanation
Indices: 1293351--1293395 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
1293341 TTTGGTAGGA
* * *
1293351 TGAATG TGAA-G TGAATG TGAAGG TGAAAG TGAAGG TGAAGG TGAA
1 TGAAGG TGAAGG TGAAGG TGAAGG TGAAGG TGAAGG TGAAGG TGAA
1293396 TCTTATTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (6 bp):
TGAAGG
Found at i:1293382 original size:12 final size:12
Alignment explanation
Indices: 1293351--1293395 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1293341 TTTGGTAGGA
1293351 TGAATGTGAA-G
1 TGAATGTGAAGG
1293362 TGAATGTGAAGG
1 TGAATGTGAAGG
*
1293374 TGAAAGTGAAGG
1 TGAATGTGAAGG
*
1293386 TGAAGGTGAA
1 TGAATGTGAA
1293396 TCTTATTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (12 bp):
TGAATGTGAAGG
Found at i:1293382 original size:18 final size:18
Alignment explanation
Indices: 1293359--1293395 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1293349 GATGAATGTG
*
1293359 AAGTGAATGTGAAGGTGA
1 AAGTGAAGGTGAAGGTGA
1293377 AAGTGAAGGTGAAGGTGA
1 AAGTGAAGGTGAAGGTGA
1293395 A
1 A
1293396 TCTTATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (18 bp):
AAGTGAAGGTGAAGGTGA
Found at i:1300963 original size:50 final size:51
Alignment explanation
Indices: 1300795--1300979 Score: 239
Period size: 51 Copynumber: 3.6 Consensus size: 51
1300785 CTATAAACAA
* * * *
1300795 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-GATAGATAATGGTCAC
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAAGAT-TTGGTCAC
* * ** * *
1300846 ATGTGTAGTACTATGTGCAAGCTACTATATGTACCGGAAGGTTTTGGTCAC
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAAGATTTGGTCAC
*
1300897 GTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAG-TTTGGTCAC
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAAGATTTGGTCAC
*
1300947 GTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTA
1300980 TCGAGTGATA
Statistics
Matches: 115, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
50 40 0.35
51 71 0.62
52 4 0.03
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (51 bp):
GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAAGATTTGGTCAC
Found at i:1301204 original size:13 final size:13
Alignment explanation
Indices: 1301186--1301212 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1301176 TAAATGAGTG
1301186 AAATTGAAACAGA
1 AAATTGAAACAGA
1301199 AAATTGAAACAGA
1 AAATTGAAACAGA
1301212 A
1 A
1301213 CAGATTACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (13 bp):
AAATTGAAACAGA
Found at i:1321819 original size:17 final size:17
Alignment explanation
Indices: 1321793--1321832 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1321783 CCAATGCACT
*
1321793 AAAATGAAAATGTAATG
1 AAAATAAAAATGTAATG
1321810 AAAATAAAAATGTAATG
1 AAAATAAAAATGTAATG
*
1321827 ATAATA
1 AAAATA
1321833 TATACTTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (17 bp):
AAAATAAAAATGTAATG
Found at i:1321994 original size:5 final size:5
Alignment explanation
Indices: 1321984--1322016 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
1321974 TGGAGCGTTT
1321984 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
1322017 GGGCTTTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:1332956 original size:106 final size:106
Alignment explanation
Indices: 1332354--1332933 Score: 838
Period size: 106 Copynumber: 5.5 Consensus size: 106
1332344 TTACAAGTGA
* * * * * *
1332354 TGATATGATAAAGGTTAGCTGATTTAATATCGCAATCTAAGTTTCTTTGAGTTAGTTTATTTAAG
1 TGATATTATAAAGGTTAGCTGATTTAAGATCACAACCTAAGTTTCTTTGAGTTAGCTGATTTAAG
* **
1332419 ATCACAACTCCTAAAACAGCTTGATGACCTACGTTCACAGC
66 ATCGCAACTCCTAAAACAGCTCAATGACCTACGTTCACAGC
*
1332460 TGATATTATAAAGGTTAGCTGATTTACGATCACAACCTAAGTTTCTTTGAGTTAGCTGATTTAAG
1 TGATATTATAAAGGTTAGCTGATTTAAGATCACAACCTAAGTTTCTTTGAGTTAGCTGATTTAAG
* * * *
1332525 ACCGGAACTCCTAAAATAGCTCAATGACCTACGTTCATAGC
66 ATCGCAACTCCTAAAACAGCTCAATGACCTACGTTCACAGC
* * * *
1332566 TGATATTATAAAGGTTAGTTGATTTAAGA-CTGCAACCTAAGTTTTTTTGAGTTAGCTGATTTGA
1 TGATATTATAAAGGTTAGCTGATTTAAGATC-ACAACCTAAGTTTCTTTGAGTTAGCTGATTTAA
* * *
1332630 GATCGCAACTCCTAAAACATCTCACTAACCTACGTTCACAGC
65 GATCGCAACTCCTAAAACAGCTCAATGACCTACGTTCACAGC
* * *
1332672 TGATATTATAAAGGTTAGCTGATTTAAGATCACAACCTAAGCTTCTTTGAGTTAGCTAATTTAAT
1 TGATATTATAAAGGTTAGCTGATTTAAGATCACAACCTAAGTTTCTTTGAGTTAGCTGATTTAAG
* *
1332737 ATCGCAACTCCTAAAATAGCTCAATGACCTACGTTTACAGC
66 ATCGCAACTCCTAAAACAGCTCAATGACCTACGTTCACAGC
* *
1332778 TAATATTATAAAGGTTAGCTGATTTAAGATCACAACCTAAGTTTCTTTGAGTTAGCTGATTTGAG
1 TGATATTATAAAGGTTAGCTGATTTAAGATCACAACCTAAGTTTCTTTGAGTTAGCTGATTTAAG
* **
1332843 ATTGCAACTCCTAAAACAGCTCGCTGACCTACGTTCACAGC
66 ATCGCAACTCCTAAAACAGCTCAATGACCTACGTTCACAGC
* * *
1332884 TGATATGATAAAGGTTAGCTGATTTAAAATCACAACCTAAGTTTATTTGA
1 TGATATTATAAAGGTTAGCTGATTTAAGATCACAACCTAAGTTTCTTTGA
1332934 ATTTGTTCCT
Statistics
Matches: 420, Mismatches: 52, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
105 1 0.00
106 418 1.00
107 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (106 bp):
TGATATTATAAAGGTTAGCTGATTTAAGATCACAACCTAAGTTTCTTTGAGTTAGCTGATTTAAG
ATCGCAACTCCTAAAACAGCTCAATGACCTACGTTCACAGC
Found at i:1352399 original size:15 final size:15
Alignment explanation
Indices: 1352373--1352411 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1352363 ATTAATAAAA
1352373 AAATATTTTTTTTTAG
1 AAATA-TTTTTTTTAG
**
1352389 AAATATTTTTTTTTT
1 AAATATTTTTTTTAG
1352404 AAATATTT
1 AAATATTT
1352412 GATGACATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
AAATATTTTTTTTAG
Found at i:1352400 original size:17 final size:16
Alignment explanation
Indices: 1352373--1352411 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1352363 ATTAATAAAA
1352373 AAATATTTTTTTTTAG
1 AAATATTTTTTTTTAG
*
1352389 AAATATTTTTTTTT-T
1 AAATATTTTTTTTTAG
1352404 AAATATTT
1 AAATATTT
1352412 GATGACATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
AAATATTTTTTTTTAG
Found at i:1354846 original size:68 final size:68
Alignment explanation
Indices: 1354734--1354995 Score: 337
Period size: 68 Copynumber: 3.9 Consensus size: 68
1354724 TCGAAATTAA
* * *
1354734 GAGTCCGCCAAGACATTAAACATGGATTCATAATGTGTAAGACCATAGCTAGGATATGACAATAT
1 GAGTCCGCCAAGACATTAAACATGGGTTCATAATGTGTAAGACCATAGCTAGGCTATGACAACAT
1354799 ATG
66 ATG
* * * * *
1354802 AAGTCCTCCAAGACATTAAACATGAGTTTATAATGTGTATGACCATAGCTAGGCTATGACAACAT
1 GAGTCCGCCAAGACATTAAACATGGGTTCATAATGTGTAAGACCATAGCTAGGCTATGACAACAT
1354867 ATG
66 ATG
* * * * * *
1354870 GAGTTCGCTAGGACATTAAACATGGGTTCATACTGTGTAAGACCATACCTAGGCTATGGCAACAT
1 GAGTCCGCCAAGACATTAAACATGGGTTCATAATGTGTAAGACCATAGCTAGGCTATGACAACAT
1354935 ATG
66 ATG
** * * *
1354938 GAGTCTACCAAAACATTAAACATGGGTTCATACAT-TGTAAGACCATAGTTGGGCTATG
1 GAGTCCGCCAAGACATTAAACATGGGTTCATA-ATGTGTAAGACCATAGCTAGGCTATG
1354996 GTGCCAGATA
Statistics
Matches: 164, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
68 163 0.99
69 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (68 bp):
GAGTCCGCCAAGACATTAAACATGGGTTCATAATGTGTAAGACCATAGCTAGGCTATGACAACAT
ATG
Found at i:1356649 original size:29 final size:29
Alignment explanation
Indices: 1356607--1356711 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
1356597 CACCATCGGT
*
1356607 ACATAGTACCTGATAAATATAAAACTGAA
1 ACATAGTACCTGATAAATATAACACTGAA
* * * * *
1356636 ACATAGTGCTTGATAACTATAACACCGAT
1 ACATAGTACCTGATAAATATAACACTGAA
*
1356665 ACAAAGTACCTGATAAATATAATCACT-AA
1 ACATAGTACCTGATAAATATAA-CACTGAA
*
1356694 CACATAGTGCCTGATAAA
1 -ACATAGTACCTGATAAA
1356712 CCTTAATGAC
Statistics
Matches: 60, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
29 42 0.70
30 18 0.30
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (29 bp):
ACATAGTACCTGATAAATATAACACTGAA
Found at i:1360393 original size:40 final size:40
Alignment explanation
Indices: 1360336--1360416 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
1360326 CTCGAGAGTG
1360336 TTAGTTAACCTAAGGTTAAGGACAACGACTACCTCAAGTC
1 TTAGTTAACCTAAGGTTAAGGACAACGACTACCTCAAGTC
*
1360376 TTAGTTAACCTAGGGTTAAGGACAACGACTACCTCAAGTC
1 TTAGTTAACCTAAGGTTAAGGACAACGACTACCTCAAGTC
1360416 T
1 T
1360417 ATAAATAGGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (40 bp):
TTAGTTAACCTAAGGTTAAGGACAACGACTACCTCAAGTC
Found at i:1369116 original size:22 final size:22
Alignment explanation
Indices: 1369058--1369109 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1369048 TGTAACACCC
*
1369058 TGAATTTTAGGGTTAGAAGTTT
1 TGAATTTTAGGGTTAAAAGTTT
* *
1369080 TGACTTTTGGGGTTAAAAGTTT
1 TGAATTTTAGGGTTAAAAGTTT
1369102 TGAATTTT
1 TGAATTTT
1369110 TCGGTTAGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (22 bp):
TGAATTTTAGGGTTAAAAGTTT
Found at i:1381784 original size:14 final size:15
Alignment explanation
Indices: 1381755--1381786 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1381745 AAAAACATCA
1381755 TAATTTTATCTATTT
1 TAATTTTATCTATTT
1381770 TAATTTTAT-TATTT
1 TAATTTTATCTATTT
1381784 TAA
1 TAA
1381787 CTATAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTATCTATTT
Found at i:1384709 original size:59 final size:59
Alignment explanation
Indices: 1384632--1384750 Score: 175
Period size: 59 Copynumber: 2.0 Consensus size: 59
1384622 GCATACATTA
* * * *
1384632 AACCTACAGGGGAGACACGGTCATGTCGCCTAGCCGTGTGTGACACACAGCTGAGTCAG
1 AACCTACAAGGGACACACGGTCATGTCGCCTAGACGTGTGTCACACACAGCTGAGTCAG
* * *
1384691 AACCTACAAGGGACACACGGTCGTGTCGCCTGGACGTGTGTCACACACGGCTGAGTCAG
1 AACCTACAAGGGACACACGGTCATGTCGCCTAGACGTGTGTCACACACAGCTGAGTCAG
1384750 A
1 A
1384751 CGCTCGTGTC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.25, C:0.28, G:0.30, T:0.17
Consensus pattern (59 bp):
AACCTACAAGGGACACACGGTCATGTCGCCTAGACGTGTGTCACACACAGCTGAGTCAG
Found at i:1385594 original size:40 final size:41
Alignment explanation
Indices: 1385516--1385660 Score: 213
Period size: 41 Copynumber: 3.6 Consensus size: 41
1385506 AAGTATAGAT
1385516 AGGGGCACGTATGTGCAATTCAAGGGTATCGAAGTACAAAC
1 AGGGGCACGTATGTGCAATTCAAGGGTATCGAAGTACAAAC
* * * *
1385557 AGAGGCACTTATGTGC-ATTCAAGGGTA-CTGAAATACAAAT
1 AGGGGCACGTATGTGCAATTCAAGGGTATC-GAAGTACAAAC
* *
1385597 AGGGGCACGTATGTGAAATTCAGGGGTATCGAAGTACAAAC
1 AGGGGCACGTATGTGCAATTCAAGGGTATCGAAGTACAAAC
1385638 AGGGGCACGTATGTGCAATTCAA
1 AGGGGCACGTATGTGCAATTCAA
1385661 CATTATTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 33 0.37
41 54 0.61
42 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.21
Consensus pattern (41 bp):
AGGGGCACGTATGTGCAATTCAAGGGTATCGAAGTACAAAC
Found at i:1400481 original size:50 final size:51
Alignment explanation
Indices: 1400366--1400482 Score: 137
Period size: 50 Copynumber: 2.3 Consensus size: 51
1400356 GATCATAACA
* ***
1400366 TGCCAAAGCCATGTCCCAAACATGGTCTTAAATGGGGTGTTCTCATATCGG
1 TGCCAAAGCCATGTCCCAAACATGGTCTTAAAGGGGGACCTCTCATATCGG
* * * * *
1400417 TGCCCATGCCATGTCCCAGACATGGTCTT-ACGGGGGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAAACATGGTCTTAAAGGGGGACCTCTCATATCGG
*
1400467 TGCCAACGCCATGTCC
1 TGCCAAAGCCATGTCC
1400483 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
50 29 0.53
51 26 0.47
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.25
Consensus pattern (51 bp):
TGCCAAAGCCATGTCCCAAACATGGTCTTAAAGGGGGACCTCTCATATCGG
Found at i:1400956 original size:27 final size:27
Alignment explanation
Indices: 1400896--1400956 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
1400886 CTCACATTTA
*
1400896 TCAAAACAGCCCTCGACTCTAACTTTT
1 TCAAAATAGCCCTCGACTCTAACTTTT
1400923 TCAAAATAGCCCTCGACTCTAACTTTT
1 TCAAAATAGCCCTCGACTCTAACTTTT
1400950 TCAAAAT
1 TCAAAAT
1400957 TATGATTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.31
Consensus pattern (27 bp):
TCAAAATAGCCCTCGACTCTAACTTTT
Found at i:1406409 original size:28 final size:27
Alignment explanation
Indices: 1406346--1406415 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 27
1406336 CCTTGCCTGA
1406346 ATATAT-TATGTTATAAAAAATATTAT
1 ATATATATATGTTATAAAAAATATTAT
*
1406372 AT-TAATTATATG-TATTAAATAATAATTAT
1 ATAT-A-TATATGTTA-TAAAAAAT-ATTAT
1406401 ATATATATAT-TTATA
1 ATATATATATGTTATA
1406416 TTTATATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
25 1 0.03
26 3 0.08
27 5 0.14
28 18 0.50
29 8 0.22
30 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATATATATGTTATAAAAAATATTAT
Found at i:1409666 original size:28 final size:29
Alignment explanation
Indices: 1409632--1409699 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 29
1409622 TAGTTTTTAG
*
1409632 GTTTAGGGTTTGTG-GTTTTTAAGTTAATT
1 GTTTAGGGTTTG-GAGTTTTTAAGTTAAGT
*
1409661 G-TTAGGGTTTGGAGTTTTTAAGTTTAGT
1 GTTTAGGGTTTGGAGTTTTTAAGTTAAGT
1409689 GTTTAGGGTTT
1 GTTTAGGGTTT
1409700 TTAGGTTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 1 0.03
28 24 0.69
29 10 0.29
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (29 bp):
GTTTAGGGTTTGGAGTTTTTAAGTTAAGT
Found at i:1409683 original size:72 final size:72
Alignment explanation
Indices: 1409590--1409724 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
1409580 GTTTTTAAGT
* * *
1409590 TTAGGGTTTGTGGTTTTTAAGTTAAGGGTTTATAGTTTTTAGGTTTAGGGTTTGTGGTTTTTAAG
1 TTAGGGTTTGTGGTTTTTAAGTTAAGGGTTTAGAGTTTTTAGGTTTAGGGTTTGGGGGTTTTAAG
1409655 TTAATTG
66 TTAATTG
* * * *
1409662 TTAGGGTTTG-GAGTTTTTAAGTTTAGTGTTTAGGGTTTTTAGGTTTAGGTTTTGGGGGTTTTA
1 TTAGGGTTTGTG-GTTTTTAAGTTAAGGGTTTAGAGTTTTTAGGTTTAGGGTTTGGGGGTTTTA
1409725 GGTTTAGGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 1 0.02
72 54 0.98
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (72 bp):
TTAGGGTTTGTGGTTTTTAAGTTAAGGGTTTAGAGTTTTTAGGTTTAGGGTTTGGGGGTTTTAAG
TTAATTG
Found at i:1409692 original size:22 final size:22
Alignment explanation
Indices: 1409579--1409656 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
1409569 AACGGTTTAG
1409579 GGTTTTTAAGTTTAGGGTTTGT
1 GGTTTTTAAGTTTAGGGTTTGT
* *
1409601 GGTTTTTAAGTTAAGGGTTTAT
1 GGTTTTTAAGTTTAGGGTTTGT
* *
1409623 AGTTTTTAGGTTTAGGGTTTGT
1 GGTTTTTAAGTTTAGGGTTTGT
1409645 GGTTTTTAAGTT
1 GGTTTTTAAGTT
1409657 AATTGTTAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (22 bp):
GGTTTTTAAGTTTAGGGTTTGT
Found at i:1409699 original size:22 final size:22
Alignment explanation
Indices: 1409664--1409778 Score: 90
Period size: 22 Copynumber: 5.3 Consensus size: 22
1409654 GTTAATTGTT
*
1409664 AGGGTTT-GGAGTTTTTAAGTTT
1 AGGGTTTAGG-GTTTTTAAGTTA
* * *
1409686 AGTGTTTAGGGTTTTTAGGTTT
1 AGGGTTTAGGGTTTTTAAGTTA
* * * * *
1409708 AGGTTTTGGGGGTTTTAGGTTT
1 AGGGTTTAGGGTTTTTAAGTTA
* * *
1409730 AGGGTTTAAGGTTTTTAGGTTT
1 AGGGTTTAGGGTTTTTAAGTTA
*
1409752 AGAGTTTAGGG-TTTTAAGTTA
1 AGGGTTTAGGGTTTTTAAGTTA
1409773 AGGGTT
1 AGGGTT
1409779 AGGATTAGGG
Statistics
Matches: 77, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.17
22 62 0.81
23 2 0.03
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (22 bp):
AGGGTTTAGGGTTTTTAAGTTA
Found at i:1409729 original size:94 final size:94
Alignment explanation
Indices: 1409572--1409746 Score: 228
Period size: 94 Copynumber: 1.9 Consensus size: 94
1409562 CAGTATTAAC
* *
1409572 GGTTTAGGGTTTTTAAGTTTAGGGTTTGTGGTTTTTAAGTTAAGGGTTTATAGTTTTTAGGTTTA
1 GGTTTAGGGTTTTTAAGTTTAGGGTTTGTGGTTTTTAAGTTAAGGGTTTAGAGGTTTTAGGTTTA
**
1409637 GGGTTTGTGGTTTTTAAGTTAATTGTTAG
66 GGGTTTAAGGTTTTTAAGTTAATTGTTAG
* * * * * *
1409666 GGTTT-GGAGTTTTTAAGTTTAGTGTTTAG-GGTTTTTAGGTTTAGGTTTTGGGGGTTTTAGGTT
1 GGTTTAGG-GTTTTTAAGTTTAGGGTTT-GTGGTTTTTAAGTTAAGGGTTTAGAGGTTTTAGGTT
1409729 TAGGGTTTAAGGTTTTTA
64 TAGGGTTTAAGGTTTTTA
1409747 GGTTTAGAGT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
93 2 0.03
94 66 0.96
95 1 0.01
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (94 bp):
GGTTTAGGGTTTTTAAGTTTAGGGTTTGTGGTTTTTAAGTTAAGGGTTTAGAGGTTTTAGGTTTA
GGGTTTAAGGTTTTTAAGTTAATTGTTAG
Found at i:1409730 original size:44 final size:44
Alignment explanation
Indices: 1409662--1409778 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 44
1409652 AAGTTAATTG
* * * *
1409662 TTAGGGTTTGGAGTTTTTAAGTTTAGTGTTTAGGGTTTTTAGGT
1 TTAGGTTTTGGAGGTTTTAAGTTTAGGGTTTAAGGTTTTTAGGT
* *
1409706 TTAGGTTTTGGGGGTTTTAGGTTTAGGGTTTAAGGTTTTTAGGT
1 TTAGGTTTTGGAGGTTTTAAGTTTAGGGTTTAAGGTTTTTAGGT
* *
1409750 TTAGAG-TTTAG-GGTTTTAAGTTAAGGGTT
1 TTAG-GTTTTGGAGGTTTTAAGTTTAGGGTT
1409779 AGGATTAGGG
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
43 16 0.25
44 46 0.73
45 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (44 bp):
TTAGGTTTTGGAGGTTTTAAGTTTAGGGTTTAAGGTTTTTAGGT
Found at i:1410082 original size:21 final size:21
Alignment explanation
Indices: 1410058--1410104 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1410048 TTTTGTCCAG
*
1410058 CTTCCGGCGGCGATTGTGGTT
1 CTTCCGGCGGCGATTCTGGTT
* *
1410079 CTTCCGGTGGGGATTCTGGTT
1 CTTCCGGCGGCGATTCTGGTT
1410100 CTTCC
1 CTTCC
1410105 AATAGGGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.26, G:0.34, T:0.36
Consensus pattern (21 bp):
CTTCCGGCGGCGATTCTGGTT
Found at i:1410854 original size:20 final size:20
Alignment explanation
Indices: 1410829--1410866 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1410819 GTTTGTTTTA
1410829 TTTTTCTTTCTCTGATATAT
1 TTTTTCTTTCTCTGATATAT
1410849 TTTTTCTTTCTCTGATAT
1 TTTTTCTTTCTCTGATAT
1410867 CCCAGTAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.16, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTTTCTTTCTCTGATATAT
Found at i:1411990 original size:13 final size:13
Alignment explanation
Indices: 1411950--1411990 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1411940 TGCATAGGCA
1411950 TTCTTTCTTACAT
1 TTCTTTCTTACAT
*
1411963 TTATTTCTGTA-AT
1 TTCTTTCT-TACAT
1411976 TTCTTTCTTACAT
1 TTCTTTCTTACAT
1411989 TT
1 TT
1411991 GTATTTATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.63
Consensus pattern (13 bp):
TTCTTTCTTACAT
Found at i:1412097 original size:19 final size:19
Alignment explanation
Indices: 1412059--1412098 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1412049 TATAATTACT
*
1412059 TACATGAATATAATTTTAA
1 TACATGAATATAATTATAA
1412078 TACATGAATAT-ATATATAA
1 TACATGAATATAAT-TATAA
1412097 TA
1 TA
1412099 TATTCAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (19 bp):
TACATGAATATAATTATAA
Found at i:1414102 original size:9 final size:9
Alignment explanation
Indices: 1414088--1414118 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1414078 GGTTGCAAAA
1414088 AGGACGATG
1 AGGACGATG
1414097 AGGACGATG
1 AGGACGATG
*
1414106 AAGACGATG
1 AGGACGATG
1414115 AGGA
1 AGGA
1414119 TAATGATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.42, T:0.10
Consensus pattern (9 bp):
AGGACGATG
Found at i:1414124 original size:18 final size:18
Alignment explanation
Indices: 1414090--1414124 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1414080 TTGCAAAAAG
*
1414090 GACGATGAGGACGATGAA
1 GACGATGAGGACAATGAA
*
1414108 GACGATGAGGATAATGA
1 GACGATGAGGACAATGA
1414125 TGTTTCTTCG
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:0.40, C:0.09, G:0.37, T:0.14
Consensus pattern (18 bp):
GACGATGAGGACAATGAA
Found at i:1416890 original size:11 final size:12
Alignment explanation
Indices: 1416874--1416928 Score: 73
Period size: 11 Copynumber: 4.8 Consensus size: 12
1416864 ATTAAATACG
1416874 AATTTGAGA-GA
1 AATTTGAGAGGA
1416885 AATTTG-GAAGGA
1 AATTTGAG-AGGA
1416897 AA-TTGAGAGGA
1 AATTTGAGAGGA
1416908 AA-TTGAGAGGA
1 AATTTGAGAGGA
1416919 AATTTGAGAG
1 AATTTGAGAG
1416929 AGGATTTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.03
11 27 0.68
12 12 0.30
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.24
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:1425253 original size:146 final size:147
Alignment explanation
Indices: 1425089--1425383 Score: 583
Period size: 146 Copynumber: 2.0 Consensus size: 147
1425079 ATTATTTTAC
1425089 AATTTTTTTTTTATGTTTTAACAATTTAAATATAATAGCATATCGAGAACATACTGCAGGCATTT
1 AATTTTTTTTTTATGTTTTAACAATTTAAATATAATAGCATATCGAGAACATACTGCAGGCATTT
1425154 ATCTAATAATAGTTATAAAGTTATCCCCGGGTTGCTTGGTTTATAATTTGAGATGGTTTTATGAT
66 ATCTAATAATAGTTATAAAGTTATCCCCGGGTTGCTTGGTTTATAATTTGAGATGGTTTTATGAT
1425219 AACTAAGTAATGCCATT
131 AACTAAGTAATGCCATT
1425236 AATTTTTTTTTT-TGTTTTAACAATTTAAATATAATAGCATATCGAGAACATACTGCAGGCATTT
1 AATTTTTTTTTTATGTTTTAACAATTTAAATATAATAGCATATCGAGAACATACTGCAGGCATTT
1425300 ATCTAATAATAGTTATAAAGTTATCCCCGGGTTGCTTGGTTTATAATTTGAGATGGTTTTATGAT
66 ATCTAATAATAGTTATAAAGTTATCCCCGGGTTGCTTGGTTTATAATTTGAGATGGTTTTATGAT
1425365 AACTAAGTAATGCCATT
131 AACTAAGTAATGCCATT
1425382 AA
1 AA
1425384 CTAATGTTTT
Statistics
Matches: 148, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
146 136 0.92
147 12 0.08
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (147 bp):
AATTTTTTTTTTATGTTTTAACAATTTAAATATAATAGCATATCGAGAACATACTGCAGGCATTT
ATCTAATAATAGTTATAAAGTTATCCCCGGGTTGCTTGGTTTATAATTTGAGATGGTTTTATGAT
AACTAAGTAATGCCATT
Found at i:1427479 original size:18 final size:18
Alignment explanation
Indices: 1427456--1427493 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1427446 TCATAATCAC
1427456 TTGAAAATTTCTTTTCAT
1 TTGAAAATTTCTTTTCAT
1427474 TTGAAAATTTCTTTTCAT
1 TTGAAAATTTCTTTTCAT
1427492 TT
1 TT
1427494 CTCATCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (18 bp):
TTGAAAATTTCTTTTCAT
Found at i:1432285 original size:45 final size:45
Alignment explanation
Indices: 1432221--1432408 Score: 220
Period size: 45 Copynumber: 4.2 Consensus size: 45
1432211 TACTACGTGT
* *
1432221 ACTGGGTACCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCC
1 ACTGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* * *
1432266 ACTGGGTATGATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC
1 ACTGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* * * *
1432311 ACCGGGTA-CTATTAATTATGAAGGTGGTTGCTATGTGTTGATTCC
1 ACTGGGTATC-ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* * * *
1432356 ACCGAGTATCATTGACTATAAGGGTGG-TGCTATGTGCTGA-TCC
1 ACTGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
*
1432399 ACTGTGTATC
1 ACTGGGTATC
1432409 TGTTATTATT
Statistics
Matches: 123, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
43 11 0.09
44 12 0.10
45 99 0.80
46 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.36
Consensus pattern (45 bp):
ACTGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
Found at i:1441081 original size:44 final size:43
Alignment explanation
Indices: 1440957--1441082 Score: 144
Period size: 44 Copynumber: 2.9 Consensus size: 43
1440947 TACCATGGTG
* * *
1440957 AATCTTATCACCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAC
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCCAC
* * * *
1441000 AATCCTTATCTCTTTGAAGTTGCAATGGAGAAGATTGAAGCCATT
1 AAT-CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCCA-C
* * *
1441045 AATCTTATCTCCTTGAAGTTTCGGTGGAGCATATTGAA
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAA
1441083 ACAAAAAATC
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 3 0.04
44 62 0.91
45 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (43 bp):
AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCCAC
Found at i:1441317 original size:95 final size:96
Alignment explanation
Indices: 1441206--1441378 Score: 276
Period size: 95 Copynumber: 1.8 Consensus size: 96
1441196 TATCTCCCTG
*
1441206 AAGTTACAGTTGAGCAGATTGAAGATAACAAATCTTATC-TTATGAAGTTGCAGTAGAGCAGATT
1 AAGTTACAGTAGAGCAGATTGAAGATAACAAATCTTATCTTTATGAAGTTGCAGTAGAGCAGATT
1441270 AAAGCTACAAACCACAAATCTTATACCCCCA
66 AAAGCTACAAACCACAAATCTTATACCCCCA
* * * *
1441301 AAGTTGCAGTAGAGCAGATTGAAGATAGCAAATCTTATCTTTCTGAAGTTGCAGTAGAGCATATT
1 AAGTTACAGTAGAGCAGATTGAAGATAACAAATCTTATCTTTATGAAGTTGCAGTAGAGCAGATT
* *
1441366 AAAGTTATAAACC
66 AAAGCTACAAACC
1441379 TTACCCCTGA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
95 36 0.51
96 34 0.49
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (96 bp):
AAGTTACAGTAGAGCAGATTGAAGATAACAAATCTTATCTTTATGAAGTTGCAGTAGAGCAGATT
AAAGCTACAAACCACAAATCTTATACCCCCA
Found at i:1441333 original size:45 final size:44
Alignment explanation
Indices: 1441182--1441543 Score: 176
Period size: 44 Copynumber: 8.0 Consensus size: 44
1441172 CTAAAGCTAC
* * * *
1441182 AAGATAGCTAATCTTATCTCCCTGAAGTTACAGTTGAGCAGATTG
1 AAGATAACAAATCTTATC-CCCTGAAGTTGCAGTAGAGCAGATTG
*** *
1441227 AAGATAACAAATCTTATCTTATGAAGTTGCAGTAGAGCAGATTA
1 AAGATAACAAATCTTATCCCCTGAAGTTGCAGTAGAGCAGATTG
* **
1441271 AAGCTACAAACCACAAATCTTATACCCCCAAAGTTGCAGTAGAGCAGATTG
1 AAG----ATA--ACAAATCTTAT-CCCCTGAAGTTGCAGTAGAGCAGATTG
* ** * *
1441322 AAGATAGCAAATCTTATCTTTCTGAAGTTGCAGTAGAGCATATTA
1 AAGATAACAAATCTTATC-CCCTGAAGTTGCAGTAGAGCAGATTG
* * *
1441367 AAG-TTATAAACCTTA-CCCCTGAAGTTGCAGT-GAGACAGATTG
1 AAGATAACAAATCTTATCCCCTGAAGTTGCAGTAGAG-CAGATTG
* * * * * * ** * * *
1441409 ATGGT-ATAGATCTTATTTCCCTAAAGTTATAGTGGAGTAGATCG
1 AAGATAACAAATCTTA-TCCCCTGAAGTTGCAGTAGAGCAGATTG
* ** ** * *
1441453 AAGATAGCAAATCTTATCTTTCTGAAGTTATAGTAGAGTAGATTA
1 AAGATAACAAATCTTATC-CCCTGAAGTTGCAGTAGAGCAGATTG
* * * * * * *
1441498 AAGGT-ATAAACCTTATCTCTCTGAAGTTACAGTGGAGAAGATTG
1 AAGATAACAAATCTTATC-CCCTGAAGTTGCAGTAGAGCAGATTG
1441542 AA
1 AA
1441544 ATGATAAGTC
Statistics
Matches: 241, Mismatches: 61, Indels: 31
0.72 0.18 0.09
Matches are distributed among these distances:
41 3 0.01
42 28 0.12
43 2 0.01
44 86 0.36
45 83 0.34
47 2 0.01
48 2 0.01
50 11 0.05
51 24 0.10
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (44 bp):
AAGATAACAAATCTTATCCCCTGAAGTTGCAGTAGAGCAGATTG
Found at i:1441540 original size:44 final size:44
Alignment explanation
Indices: 1441301--1441540 Score: 144
Period size: 45 Copynumber: 5.5 Consensus size: 44
1441291 TATACCCCCA
* * * * * * *
1441301 AAGTTGCAGTAGAGCAGATTGAAGATAGCAAATCTTATCTTTCTG
1 AAGTTACAGTAGAGAAGATTAAAGGTA-TAAACCTTATCTCTCTG
* * * * *
1441346 AAGTTGCAGTAGAGCATATTAAAGTTATAAACCTTA-C-CCCTG
1 AAGTTACAGTAGAGAAGATTAAAGGTATAAACCTTATCTCTCTG
* * * * * * * *
1441388 AAGTTGCAGT-GAGACAGATTGATGGTATAGATCTTATTTCCCTA
1 AAGTTACAGTAGAGA-AGATTAAAGGTATAAACCTTATCTCTCTG
* * * ** * * * *
1441432 AAGTTATAGTGGAGTAGATCGAAGATAGCAAATCTTATCTTTCTG
1 AAGTTACAGTAGAGAAGATTAAAGGTA-TAAACCTTATCTCTCTG
* *
1441477 AAGTTATAGTAGAGTAGATTAAAGGTATAAACCTTATCTCTCTG
1 AAGTTACAGTAGAGAAGATTAAAGGTATAAACCTTATCTCTCTG
*
1441521 AAGTTACAGTGGAGAAGATT
1 AAGTTACAGTAGAGAAGATT
1441541 GAAATGATAA
Statistics
Matches: 152, Mismatches: 38, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
41 3 0.02
42 28 0.18
43 1 0.01
44 59 0.39
45 61 0.40
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (44 bp):
AAGTTACAGTAGAGAAGATTAAAGGTATAAACCTTATCTCTCTG
Found at i:1443217 original size:52 final size:54
Alignment explanation
Indices: 1443161--1443270 Score: 156
Period size: 53 Copynumber: 2.1 Consensus size: 54
1443151 AACATTATTC
*
1443161 ATATTTGA-TTTATCAATTT-ATCATTCTTTTTAC-TTTAAAATATTTAAATTTA
1 ATATTT-ATTTTATCAATTTGATCATTATTTTTACTTTTAAAATATTTAAATTTA
* *
1443213 ATA-TTATTTTATCTATTTGTTCATTATTTTTACTTTTAAAATATTTAAATTTA
1 ATATTTATTTTATCAATTTGATCATTATTTTTACTTTTAAAATATTTAAATTTA
1443266 ATATT
1 ATATT
1443271 ATATGTATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
50 1 0.02
51 12 0.24
52 15 0.29
53 22 0.43
54 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (54 bp):
ATATTTATTTTATCAATTTGATCATTATTTTTACTTTTAAAATATTTAAATTTA
Found at i:1443266 original size:53 final size:55
Alignment explanation
Indices: 1443181--1443286 Score: 173
Period size: 53 Copynumber: 2.0 Consensus size: 55
1443171 TATCAATTTA
*
1443181 TCATTCTTTTTACTTTAAAATATTTAAATTTAATATTAT-T-T-TATCTATTTGT
1 TCATTATTTTTACTTTAAAATATTTAAATTTAATATTATATGTATATCTATTTGT
1443233 TCATTATTTTTACTTTTAAAATATTTAAATTTAATATTATATGTATATCTATTT
1 TCATTATTTTTAC-TTTAAAATATTTAAATTTAATATTATATGTATATCTATTT
1443287 ATCTCCAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
52 12 0.24
53 26 0.53
54 1 0.02
55 1 0.02
56 9 0.18
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (55 bp):
TCATTATTTTTACTTTAAAATATTTAAATTTAATATTATATGTATATCTATTTGT
Found at i:1451671 original size:4 final size:4
Alignment explanation
Indices: 1451658--1451712 Score: 69
Period size: 4 Copynumber: 13.8 Consensus size: 4
1451648 AAGGTTGAAG
*
1451658 AAAT -AAT AAAT AAAT AAAT GAAT AAAT AAAT AAAT AAAAT AAA- ATAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT A-AAT
1451706 AAAT AAA
1 AAAT AAA
1451713 ATAGTTTGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
3 4 0.09
4 36 0.80
5 5 0.11
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1453039 original size:44 final size:44
Alignment explanation
Indices: 1452972--1453157 Score: 203
Period size: 44 Copynumber: 4.2 Consensus size: 44
1452962 TGTCAGAGAA
* * *
1452972 ATAAGATTTTCTATCTTCAATCTGCTCCACTGCAACTTCAAGGAG
1 ATAAGA-TTTGTAGCTTCAATCTACTCCACTGCAACTTCAAGGAG
* *
1453017 ATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCATGGAG
1 ATAAGATTTGTAGCTTCAATCTACTCCACTGCAACTTCAAGGAG
* * * *
1453061 ATAAGATTCGTAGCTTTAATCTACTCCACTGTAACTT-TAGAGAG
1 ATAAGATTTGTAGCTTCAATCTACTCCACTGCAACTTCAAG-GAG
** * * * *
1453105 ATAAGATTCATAGCTTCAATCTATTCCACTGTAACTTTAGGGAG
1 ATAAGATTTGTAGCTTCAATCTACTCCACTGCAACTTCAAGGAG
*
1453149 ATACGATTT
1 ATAAGATTT
1453158 ACTACGATTA
Statistics
Matches: 123, Mismatches: 16, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
43 1 0.01
44 115 0.93
45 7 0.06
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (44 bp):
ATAAGATTTGTAGCTTCAATCTACTCCACTGCAACTTCAAGGAG
Found at i:1459896 original size:4 final size:4
Alignment explanation
Indices: 1459883--1459928 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
1459873 AAGGTTGAAG
* *
1459883 AAAT -AAT AAAT AAAT GAAT AAAT AAAT AACT AAA- ATAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAA
1459929 ACACTTTGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 4 0.11
4 30 0.86
5 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1465161 original size:17 final size:17
Alignment explanation
Indices: 1465139--1465172 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1465129 ATATTAATTC
1465139 AATAATATTTTTTTGAT
1 AATAATATTTTTTTGAT
1465156 AATAATATTTTTTTGAT
1 AATAATATTTTTTTGAT
1465173 TCATGTTTAA
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:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
AATAATATTTTTTTGAT
Found at i:1478847 original size:26 final size:26
Alignment explanation
Indices: 1478818--1478869 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1478808 AGGGACCTCT
1478818 CACATAGACAATCCTGGAAGACTTCC
1 CACATAGACAATCCTGGAAGACTTCC
* * *
1478844 CACATAGACAGTTCTGGCAGACTTCC
1 CACATAGACAATCCTGGAAGACTTCC
1478870 ACGTAGATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (26 bp):
CACATAGACAATCCTGGAAGACTTCC
Found at i:1479029 original size:26 final size:26
Alignment explanation
Indices: 1478968--1479037 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 26
1478958 ATGGTCCTTG
***
1478968 CAGACTTTCCCATTAGATAGTCAGTG
1 CAGACTTTCCCATTAGATAGTCACAA
* * * *
1478994 CGGACCTTCCTATTAGATAGTCCCAA
1 CAGACTTTCCCATTAGATAGTCACAA
*
1479020 CAGACTTTCCCATCAGAT
1 CAGACTTTCCCATTAGAT
1479038 GGTCCTTGTG
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (26 bp):
CAGACTTTCCCATTAGATAGTCACAA
Found at i:1485147 original size:22 final size:23
Alignment explanation
Indices: 1485101--1485147 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1485091 AACATTGAAG
*
1485101 AATTTCGATTATAATATATAGGA
1 AATTTCGATTATAATATATACGA
1485124 AATTT-GATTATAAGTAT-TACGA
1 AATTTCGATTATAA-TATATACGA
1485146 AA
1 AA
1485148 ATGATGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (23 bp):
AATTTCGATTATAATATATACGA
Found at i:1485149 original size:23 final size:23
Alignment explanation
Indices: 1485101--1485149 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
1485091 AACATTGAAG
*
1485101 AATTTCGATTATAATATATAGGA
1 AATTTCGATTATAATATATAGAA
1485124 AATTT-GATTATAAGTAT-TACGAA
1 AATTTCGATTATAA-TATATA-GAA
1485147 AAT
1 AAT
1485150 GATGTCATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (23 bp):
AATTTCGATTATAATATATAGAA
Found at i:1495725 original size:22 final size:22
Alignment explanation
Indices: 1495691--1495732 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1495681 TATATAATTA
* *
1495691 ATATTACTTGAATAGTTATGAG
1 ATATTACTCGAATAATTATGAG
*
1495713 ATATTAGTCGAATAATTATG
1 ATATTACTCGAATAATTATG
1495733 TCTCTTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (22 bp):
ATATTACTCGAATAATTATGAG
Found at i:1500401 original size:5 final size:5
Alignment explanation
Indices: 1500393--1500417 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1500383 CCCTCCTTAC
1500393 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
1500418 TCCTCCTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:1500954 original size:27 final size:27
Alignment explanation
Indices: 1500917--1501137 Score: 227
Period size: 27 Copynumber: 8.2 Consensus size: 27
1500907 CTTAGGCTAA
*
1500917 AAAATTATCGAAATACCCTCGAAGGGT
1 AAAATTATCAAAATACCCTCGAAGGGT
*
1500944 AAAATTATCGAAATACCCTCGAAGGGT
1 AAAATTATCAAAATACCCTCGAAGGGT
* * *
1500971 AAAATTATCGAAATACCATCGAATGGT
1 AAAATTATCAAAATACCCTCGAAGGGT
* * *
1500998 AAAATTACCAAAATACCC-CTATAGGGA
1 AAAATTATCAAAATACCCTCGA-AGGGT
*
1501025 AAAATTACCAAAATACCCTCGAAGGGT
1 AAAATTATCAAAATACCCTCGAAGGGT
* * *
1501052 AAAATGA-CTAATATACCCTTCGCAGGGT
1 AAAATTATC-AAAATACCC-TCGAAGGGT
* *
1501080 AAAATGATCAAAATACCCCCGAAGGGT
1 AAAATTATCAAAATACCCTCGAAGGGT
*
1501107 AAAATGA-CTAAAATACCC-C-ATAGGGT
1 AAAATTATC-AAAATACCCTCGA-AGGGT
1501133 AAAAT
1 AAAAT
1501138 GATTGATATA
Statistics
Matches: 171, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
25 1 0.01
26 15 0.09
27 129 0.75
28 25 0.15
29 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (27 bp):
AAAATTATCAAAATACCCTCGAAGGGT
Found at i:1501390 original size:26 final size:26
Alignment explanation
Indices: 1501316--1501391 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
1501306 TTACCACAAA
* * * *
1501316 TACTGTTACTGGCAACTTTGCTACGT
1 TACTATTACTGGCAGCTTTGCTGCAT
* * * *
1501342 TACTGTTATTGGAAGCTCTGCTGCAT
1 TACTATTACTGGCAGCTTTGCTGCAT
*
1501368 TATTATTACTGGCAGCTTTGCTGC
1 TACTATTACTGGCAGCTTTGCTGC
1501392 GATATTGGTG
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCAT
Found at i:1508490 original size:27 final size:27
Alignment explanation
Indices: 1508451--1508738 Score: 249
Period size: 27 Copynumber: 10.7 Consensus size: 27
1508441 CTTGGGCTAA
* **
1508451 AAAATTACTGAAATACCCTCGAAGTTT
1 AAAATTACCGAAATACCCTCGAAGGGT
* * **
1508478 AAAATTATCGAAATACACTAAAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
* *
1508505 AAACTTACCGAAATACCTTCGAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
* * * *
1508532 AAAAATATCGAAATATCCTCGACGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
* *
1508559 AAAATTATCGAAATACCCTCAAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
* * *
1508586 AAAATTATCGAAATACCC-CCATAGGAT
1 AAAATTACCGAAATACCCTCGA-AGGGT
* *
1508613 AAAATTACCAAAATACCCTCGAAGGAT
1 AAAATTACCGAAATACCCTCGAAGGGT
* * *
1508640 AAAATGACCAAAATACCCCCGAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
* * *
1508667 AAAATGACCAAAATACCCTCGAAGGAT
1 AAAATTACCGAAATACCCTCGAAGGGT
* * *
1508694 AAAATGA-CTAAATACCC-CCATAGGGT
1 AAAATTACCGAAATACCCTCGA-AGGGT
* * *
1508720 AAAATGACTGATATACCCT
1 AAAATTACCGAAATACCCT
1508739 AAGAGTTGGA
Statistics
Matches: 217, Mismatches: 39, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
25 2 0.01
26 22 0.10
27 191 0.88
28 2 0.01
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (27 bp):
AAAATTACCGAAATACCCTCGAAGGGT
Found at i:1510287 original size:17 final size:18
Alignment explanation
Indices: 1510254--1510294 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1510244 AAGGTAACCA
1510254 TTTATATTTCTATTAGT-T
1 TTTA-ATTTCTATTAGTCT
1510272 TTTAATTT-TATCTAGTCT
1 TTTAATTTCTAT-TAGTCT
1510290 TTTAA
1 TTTAA
1510295 ATGAAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.14
17 8 0.38
18 10 0.48
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTAATTTCTATTAGTCT
Found at i:1511246 original size:17 final size:17
Alignment explanation
Indices: 1511226--1511287 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
1511216 TTGAATGTTA
1511226 TGTGATTATATGAGTAT
1 TGTGATTATATGAGTAT
*
1511243 TGTGATATATGCTTGAATGT-T
1 TGTGAT-TAT--ATG-A-GTAT
1511264 ATGTGATTATATGAGTAT
1 -TGTGATTATATGAGTAT
1511282 TGTGAT
1 TGTGAT
1511288 ATAACCTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
17 14 0.39
18 5 0.14
19 2 0.06
20 2 0.06
21 5 0.14
22 8 0.22
ACGTcount: A:0.27, C:0.02, G:0.24, T:0.47
Consensus pattern (17 bp):
TGTGATTATATGAGTAT
Found at i:1511254 original size:39 final size:39
Alignment explanation
Indices: 1511199--1511334 Score: 218
Period size: 39 Copynumber: 3.5 Consensus size: 39
1511189 CATATTTTTA
*
1511199 AGTATTGTGATGTATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
1511238 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
** *
1511277 AGTATTGTGATATAACCTTAAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* *
1511316 TGTAATGTGATATATGCTT
1 AGTATTGTGATATATGCTT
1511335 AAAACTGTAT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.46
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
Found at i:1516976 original size:52 final size:52
Alignment explanation
Indices: 1516898--1517002 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
1516888 GGATTAATTG
1516898 CTTGTGGAAATAATTCAATGCATTATTTGAGAATTTAGTAGTAGCCTAGACC
1 CTTGTGGAAATAATTCAATGCATTATTTGAGAATTTAGTAGTAGCCTAGACC
1516950 CTTGTGGAAATAATTCAATGCATTATTTGAGAATTTAGTAGTAGCCTAGACC
1 CTTGTGGAAATAATTCAATGCATTATTTGAGAATTTAGTAGTAGCCTAGACC
1517002 C
1 C
1517003 CTACTCTAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (52 bp):
CTTGTGGAAATAATTCAATGCATTATTTGAGAATTTAGTAGTAGCCTAGACC
Found at i:1517074 original size:23 final size:24
Alignment explanation
Indices: 1517038--1517082 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
1517028 GTCTCATACC
1517038 TATGTTATCTTGTGAACTATGTGCT
1 TATGTTATCTTGTGAA-TATGTGCT
1517063 TATG-TAT-TTGTGAATATGTG
1 TATGTTATCTTGTGAATATGTG
1517083 AACTGAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 7 0.35
24 3 0.15
25 4 0.20
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.49
Consensus pattern (24 bp):
TATGTTATCTTGTGAATATGTGCT
Found at i:1517631 original size:39 final size:39
Alignment explanation
Indices: 1517576--1517716 Score: 210
Period size: 39 Copynumber: 3.6 Consensus size: 39
1517566 AACATGTTTT
* *
1517576 TGAGTATTGTGATATATGCTTGAATTTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
1517615 TGAGTATTGTGGTATATGCTTAAATGTTATATGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
1517654 TGAGTATTGTGACATATCCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
1517693 TGTGTAATGTGATATATGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
1517717 AATGAACATG
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 90 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:1520253 original size:4 final size:4
Alignment explanation
Indices: 1520244--1520283 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
1520234 TTTGTTTATC
*
1520244 TTTA TTTA TTTA TTTA TTTA TTTA TTTTA GTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTT
1520284 TTAGTCCTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:1520277 original size:13 final size:13
Alignment explanation
Indices: 1520233--1520284 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
1520223 TGTTTAATTC
*
1520233 ATTTGTTTATCTTT
1 ATTTATTTAT-TTT
1520247 ATTTATTTA-TTT
1 ATTTATTTATTTT
1520259 ATTTATTTATTTT
1 ATTTATTTATTTT
*
1520272 AGTTATTTATTTT
1 ATTTATTTATTTT
1520285 TAGTCCTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
12 12 0.34
13 15 0.43
14 8 0.23
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:1520278 original size:25 final size:26
Alignment explanation
Indices: 1520233--1520283 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
1520223 TGTTTAATTC
* *
1520233 ATTTGTTTATCTTTATTTATTTATTT
1 ATTTATTTATCTTTAGTTATTTATTT
1520259 ATTTATTTAT-TTTAGTTATTTATTT
1 ATTTATTTATCTTTAGTTATTTATTT
1520284 TTAGTCCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (26 bp):
ATTTATTTATCTTTAGTTATTTATTT
Found at i:1521455 original size:57 final size:58
Alignment explanation
Indices: 1521368--1521481 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 58
1521358 AGAAATGGTG
* * *
1521368 AAAATGGAGAAATAGGAAACATTTGGAAATGATTATGGTTTTCTCAAAAATGAAAATT
1 AAAATAGAGAAATACGAAACATTTGGAAATGAATATGGTTTTCTCAAAAATGAAAATT
* * *
1521426 AAAATAGAGAAAT-CGAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAAT
1 AAAATAGAGAAATACGAAACATTTGGAAATGAATATGGTTTTCTCAAAAATGAAAAT
1521482 GACATGAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 38 0.76
58 12 0.24
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (58 bp):
AAAATAGAGAAATACGAAACATTTGGAAATGAATATGGTTTTCTCAAAAATGAAAATT
Found at i:1522924 original size:28 final size:28
Alignment explanation
Indices: 1522892--1522947 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1522882 TTCATGCTTG
1522892 GTCTGTTAATTTATTTTTAAGATCCAAA
1 GTCTGTTAATTTATTTTTAAGATCCAAA
1522920 GTCTGTTAATTTATTTTTAAGATCCAAA
1 GTCTGTTAATTTATTTTTAAGATCCAAA
1522948 CTATCAATCA
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:0.11, G:0.11, T:0.46
Consensus pattern (28 bp):
GTCTGTTAATTTATTTTTAAGATCCAAA
Found at i:1525469 original size:16 final size:16
Alignment explanation
Indices: 1525448--1525493 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1525438 GGGGTCGAAC
*
1525448 TTCTCTTATTCAAATT
1 TTCTCTAATTCAAATT
*
1525464 TTCTCTAATTTAAATT
1 TTCTCTAATTCAAATT
1525480 TTCT-TGAATTCAAA
1 TTCTCT-AATTCAAA
1525494 GCTATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 1 0.04
16 25 0.96
ACGTcount: A:0.30, C:0.15, G:0.02, T:0.52
Consensus pattern (16 bp):
TTCTCTAATTCAAATT
Found at i:1526404 original size:7 final size:7
Alignment explanation
Indices: 1526392--1526447 Score: 94
Period size: 7 Copynumber: 8.0 Consensus size: 7
1526382 GTAAATAAAT
1526392 ATTATTA
1 ATTATTA
1526399 ATTATTA
1 ATTATTA
1526406 ATTATTA
1 ATTATTA
1526413 ATTATTA
1 ATTATTA
1526420 ATTATTA
1 ATTATTA
*
1526427 ATTATTT
1 ATTATTA
*
1526434 ATAATTA
1 ATTATTA
1526441 ATTATTA
1 ATTATTA
1526448 TTCAATTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTATTA
Found at i:1526456 original size:21 final size:21
Alignment explanation
Indices: 1526395--1526456 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1526385 AATAAATATT
*
1526395 ATTAATTATTAATT-ATTAATT
1 ATTAATTATTAATTAATT-ATA
*
1526416 ATTAATTATTAATTATTTATA
1 ATTAATTATTAATTAATTATA
1526437 ATTAATTATT-ATTCAATTAT
1 ATTAATTATTAATT-AATTAT
1526457 GTTTAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 3 0.08
21 31 0.86
22 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTAATTATTAATTAATTATA
Found at i:1529377 original size:22 final size:22
Alignment explanation
Indices: 1529347--1529388 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1529337 ACACCAAAAC
*
1529347 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
1529369 AGGCCTTTAGCGGCGCTTTT
1 AGGCCTTTAGCGGCGCTTTT
1529389 ATAAGTGCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.29, T:0.40
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:1529484 original size:43 final size:43
Alignment explanation
Indices: 1529424--1529688 Score: 282
Period size: 43 Copynumber: 6.2 Consensus size: 43
1529414 AAGAATGCGT
* * * *
1529424 CGCTAAAGGCCAAGACCTTTAGCGGCACTTTTCCCACAAACGT
1 CGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCACAAACGC
*
1529467 CGCTAAAGACCAGGACCTTTAGCGGCGCTTTTGCCACAAACGC
1 CGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCACAAACGC
* *
1529510 CGCTAAAGACCGGGACCTTTAGCGGTGCTTTTCCCACAAACGC
1 CGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * * *
1529553 CGCTAAAGACCATGTCCTTTAGCGGCGCTTTTACCATAAACGC
1 CGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * * * * ** *
1529596 CGCTATAGACCATGACTTTTTAGCGACGCTTCTGTCACAAACAC
1 CGCTAAAGACCAGGAC-CTTTAGCGGCGCTTTTCCCACAAACGC
* * * * *
1529640 CGCTAAAGAACA-AACCTTTAGCGACGCTTATT-GCAAAAACGC
1 CGCTAAAGACCAGGACCTTTAGCGGCGCTT-TTCCCACAAACGC
1529682 CGCTAAA
1 CGCTAAA
1529689 AATATAACCT
Statistics
Matches: 189, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
42 27 0.14
43 132 0.70
44 30 0.16
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (43 bp):
CGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCACAAACGC
Found at i:1531517 original size:23 final size:23
Alignment explanation
Indices: 1531467--1531518 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1531457 GTTAGGTGTC
* *
1531467 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
1531490 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
1531513 AGTATG
1 AGTATG
1531519 TTCAATTGCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:1537012 original size:28 final size:29
Alignment explanation
Indices: 1536974--1537045 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
1536964 TCTGACCCCG
* * *
1536974 AACCTCTAAACCTTAAA-TCACTAACTGTT
1 AACCCCTAAACCTTAAACTC-CTAACCGCT
**
1537003 AACCCC-AAACCCCAAACTCCTAACCGCT
1 AACCCCTAAACCTTAAACTCCTAACCGCT
1537031 AACCCCTAAACCTTA
1 AACCCCTAAACCTTA
1537046 TTTAATATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.38, C:0.39, G:0.03, T:0.21
Consensus pattern (29 bp):
AACCCCTAAACCTTAAACTCCTAACCGCT
Found at i:1537328 original size:14 final size:15
Alignment explanation
Indices: 1537311--1537343 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1537301 CTTAAATCAA
1537311 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
1537325 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
1537340 AATC
1 AATC
1537344 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:1537649 original size:41 final size:40
Alignment explanation
Indices: 1537572--1537980 Score: 462
Period size: 41 Copynumber: 9.9 Consensus size: 40
1537562 AAAAAAAAGG
* * *
1537572 GCATTAGCGGCGCTTTTTAAAAAAACGTCGCTAAAGGGCCG-
1 GCATTAGCGGCGC-TTTT-CAAAAACGCCGCTAAAGGCCCGA
* *
1537613 GCCATTAGCGGCGCTTCTTCAAAAATGCCGCTAAAGGGCCGA
1 G-CATTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGGCCCGA
*
1537655 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAAGGCCCCA
1 GCATTAGCGGCGCTT-TTCAAAAACGCCGCT-AAAGGCCCGA
* * *
1537697 GCATTAGCGACGCTTTACCAAAAACGTCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTT-TCAAAAACGCCGCTAAAGGCCCGA
* * *
1537738 GCATTAGCGGTGCTTTATCAAAAACGTCGCTAAAGACCCGA
1 GCATTAGCGGCGCTTT-TCAAAAACGCCGCTAAAGGCCCGA
* * *
1537779 GCATTAGCGGCCCTTTATCAAAAACACCGCTAAAGACCCGA
1 GCATTAGCGGCGCTTT-TCAAAAACGCCGCTAAAGGCCCGA
* * *
1537820 GCATTAGCGGCGCTTTATAAAAAATGCCGCTAAAGGCCCAA
1 GCATTAGCGGCGCTTT-TCAAAAACGCCGCTAAAGGCCCGA
* *
1537861 GCATTAGCGGCGCTTTTTTAAAAATG-CGCTAAAGGCCCGA
1 GCATTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGGCCCGA
* *
1537901 GCATTAGCGGCGCTTTTTTAAAAATGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGGCCCGA
* * *
1537942 GCATTAGCAGCACTTTTTCAAAAATGCCGCTAAAGGCCC
1 GCATTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGGCCC
1537981 CAAAAAATAG
Statistics
Matches: 332, Mismatches: 29, Indels: 14
0.89 0.08 0.04
Matches are distributed among these distances:
40 39 0.12
41 241 0.73
42 52 0.16
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTCAAAAACGCCGCTAAAGGCCCGA
Found at i:1538061 original size:39 final size:40
Alignment explanation
Indices: 1538016--1538142 Score: 150
Period size: 40 Copynumber: 3.2 Consensus size: 40
1538006 GGCTTTTTGT
*
1538016 GGCGTTTTACAAAAAACGCCGCTAATGCTT-ATTTTTAGC
1 GGCGTTTTACAAAAAGCGCCGCTAATGCTTGATTTTTAGC
* * * **
1538055 AGCGTTTTCCAAAAAGCGCCGCTGATGCTTGACCTTTAGC
1 GGCGTTTTACAAAAAGCGCCGCTAATGCTTGATTTTTAGC
* * *
1538095 GGCGTTTTTA-TAAAAGCGCTGCTAATGCTTGATTTTTAGT
1 GGCG-TTTTACAAAAAGCGCCGCTAATGCTTGATTTTTAGC
1538135 GGCGTTTT
1 GGCGTTTT
1538143 TTCCCAAACG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 30 0.42
40 38 0.53
41 4 0.06
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (40 bp):
GGCGTTTTACAAAAAGCGCCGCTAATGCTTGATTTTTAGC
Found at i:1538159 original size:40 final size:41
Alignment explanation
Indices: 1538027--1538159 Score: 134
Period size: 40 Copynumber: 3.3 Consensus size: 41
1538017 GCGTTTTACA
* *
1538027 AAAAACGCCGCTAATGCTT-ATTTTTAGCAGCG--TTTTCC
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTCC
* **
1538065 AAAAAGCGCCGCTGATGCTTGACCTTTAGCGGCGTTTTTAT--
1 -AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTT-TCC
* *
1538106 AAAAGCGCTGCTAATGCTTGATTTTTAGTGGCGTTTTTTCC
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTCC
*
1538147 CAAA-CGCCGCTAA
1 AAAAGCGCCGCTAA
1538160 AAATGCCGCT
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
39 18 0.24
40 51 0.67
41 3 0.04
42 3 0.04
43 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (41 bp):
AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTCC
Found at i:1538263 original size:3 final size:3
Alignment explanation
Indices: 1538255--1538288 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1538245 GATTATGCAA
1538255 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1538289 TTCTAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1539858 original size:257 final size:252
Alignment explanation
Indices: 1539391--1539906 Score: 758
Period size: 257 Copynumber: 2.0 Consensus size: 252
1539381 TTAAATGTGA
*
1539391 AAAATTTACTCGTAAATAGTGATTAAACATGCATTAGTTAATGGACGAAAAACTAATAGAGTAGA
1 AAAATCTACTCGTAAATAGTGATTAAACATGCATTAGTTAATGGACGAAAAACTAATAGAGTAGA
*
1539456 ATCAAACTCAATTTATTTGTAATAGTAATTACAGATAGATATGATAAAAAAAAAATTGAAATAGA
66 ATCAAACTCAATTTATTTGTAATAGTAATTACAGATAGATATGAT--AAAAAAAATTGAAACAGA
1539521 TTGGTTTTCATTCGATCGGATTTGATAGAGTTGGAATTTTGTTTTTTAAAATTAAGTTTGAAATG
129 TTGGTTTTCATTCGATCGGATTTGATAGAGTTGGAATTTTGTTTTTTAAAATTAAGTTTGAAATG
* *
1539586 GAGGAAGTATTTTTTTTTTTAAAATCGAGTCTAAACTCGTTCTACCTGTTTGAAATATTTAC
194 GAGGAAGTA--TTTTTTTTT-AAATCGAGTCTAAACTCATTCTACCCGTTTGAAATATTTAC
* *
1539648 AAAATCTACTTGTAAATAGTGATTAAACTTGCATTAGTTAATGGACGAACAAA-TAATAGAGTAG
1 AAAATCTACTCGTAAATAGTGATTAAACATGCATTAGTTAATGGACGAA-AAACTAATAGAGTAG
*
1539712 AATCAAACTCAATTTATTTGTAATGGTAATTACCA-ATAGATATGAT-AAAAAAATTGAAACCA-
65 AATCAAACTCAATTTATTTGTAATAGTAATTA-CAGATAGATATGATAAAAAAAATTGAAA-CAG
* * *
1539774 ATTGG-TTTCATTCGATTGGATTTGTTAGAGTT-GAATTTCTTTTTTTTTTTAAAATTAAGTTTG
128 ATTGGTTTTCATTCGATCGGATTTGATAGAGTTGGAA----TTTTGTTTTTTAAAATTAAGTTTG
*
1539837 AGA-GGAAGGAAGTTATTTTTTTTTAAATCGAGTCTAAACTCATTCTACCCGTTTGAAATATTTA
189 AAATGG-AGGAAG-TATTTTTTTTTAAATCGAGTCTAAACTCATTCTACCCGTTTGAAATATTTA
1539901 C
252 C
1539902 AAAAT
1 AAAAT
1539907 TATCTTCTCT
Statistics
Matches: 239, Mismatches: 11, Indels: 21
0.88 0.04 0.08
Matches are distributed among these distances:
252 3 0.01
253 25 0.10
254 62 0.26
255 12 0.05
256 31 0.13
257 101 0.42
258 5 0.02
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (252 bp):
AAAATCTACTCGTAAATAGTGATTAAACATGCATTAGTTAATGGACGAAAAACTAATAGAGTAGA
ATCAAACTCAATTTATTTGTAATAGTAATTACAGATAGATATGATAAAAAAAATTGAAACAGATT
GGTTTTCATTCGATCGGATTTGATAGAGTTGGAATTTTGTTTTTTAAAATTAAGTTTGAAATGGA
GGAAGTATTTTTTTTTAAATCGAGTCTAAACTCATTCTACCCGTTTGAAATATTTAC
Found at i:1550632 original size:30 final size:30
Alignment explanation
Indices: 1550591--1550651 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1550581 CTACTTCGGT
1550591 TGGTAGGGACTACCGCACCTCAAGCCAAAC
1 TGGTAGGGACTACCGCACCTCAAGCCAAAC
*
1550621 TGGTAGTGACTACCGCACCTCAAGCCAAAC
1 TGGTAGGGACTACCGCACCTCAAGCCAAAC
1550651 T
1 T
1550652 CGCTTACTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.16
Consensus pattern (30 bp):
TGGTAGGGACTACCGCACCTCAAGCCAAAC
Found at i:1552895 original size:39 final size:39
Alignment explanation
Indices: 1552845--1552940 Score: 165
Period size: 39 Copynumber: 2.5 Consensus size: 39
1552835 GGAGTTGTAA
* *
1552845 GTGACTATTCATCTACATCACTTCAGTGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
*
1552884 GTGACTATTCATCTTCATCACTTAAATGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
1552923 GTGACTATTCATCTACAT
1 GTGACTATTCATCTACAT
1552941 GCATGTGTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (39 bp):
GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
Found at i:1552991 original size:32 final size:32
Alignment explanation
Indices: 1552950--1553010 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1552940 TGCATGTGTG
*
1552950 TAACTCTTCATCTTCAAGTTTCTTCACATTTC
1 TAACTCTTCATCTTCAAGTCTCTTCACATTTC
*
1552982 TAACTCTTCATCTTCAAGTCTCTTTACAT
1 TAACTCTTCATCTTCAAGTCTCTTCACAT
1553011 ACTTAGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.23, C:0.28, G:0.03, T:0.46
Consensus pattern (32 bp):
TAACTCTTCATCTTCAAGTCTCTTCACATTTC
Found at i:1557317 original size:43 final size:41
Alignment explanation
Indices: 1557269--1557378 Score: 120
Period size: 39 Copynumber: 2.7 Consensus size: 41
1557259 CTTCATCACA
* *
1557269 TATAGGAGTTGTAAGTGACTATTCATCTACATCACTTCAGTGC
1 TATAGGAGTTGT--GTGACTATTCATCTACATCACTTAAATGC
* * *
1557312 TATAGGAG-T-TGTGACTATTTATCTTCATCATTTAAATGC
1 TATAGGAGTTGTGTGACTATTCATCTACATCACTTAAATGC
*
1557351 TATAGGAG-T-TGTGAGTATTCATCTACAT
1 TATAGGAGTTGTGTGACTATTCATCTACAT
1557379 GCATGTGTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 49 0.83
41 1 0.02
42 1 0.02
43 8 0.14
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (41 bp):
TATAGGAGTTGTGTGACTATTCATCTACATCACTTAAATGC
Found at i:1557341 original size:39 final size:39
Alignment explanation
Indices: 1557283--1557378 Score: 138
Period size: 39 Copynumber: 2.5 Consensus size: 39
1557273 GGAGTTGTAA
* *
1557283 GTGACTATTCATCTACATCACTTCAGTGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
* * *
1557322 GTGACTATTTATCTTCATCATTTAAATGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
*
1557361 GTGAGTATTCATCTACAT
1 GTGACTATTCATCTACAT
1557379 GCATGTGTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (39 bp):
GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
Found at i:1557412 original size:16 final size:16
Alignment explanation
Indices: 1557391--1557445 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
1557381 ATGTGTGTAA
1557391 CTCTTCATCTTCAAGT
1 CTCTTCATCTTCAAGT
1557407 CTCTTCA-CATTTCTAA--
1 CTCTTCATC--TTC-AAGT
*
1557423 CTCTTCATTTTCAAGT
1 CTCTTCATCTTCAAGT
1557439 CTCTTCA
1 CTCTTCA
1557446 CATACCTAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 21 0.66
17 3 0.09
18 2 0.06
ACGTcount: A:0.20, C:0.31, G:0.04, T:0.45
Consensus pattern (16 bp):
CTCTTCATCTTCAAGT
Found at i:1557429 original size:32 final size:32
Alignment explanation
Indices: 1557388--1557448 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1557378 TGCATGTGTG
1557388 TAACTCTTCATCTTCAAGTCTCTTCACATTTC
1 TAACTCTTCATCTTCAAGTCTCTTCACATTTC
*
1557420 TAACTCTTCATTTTCAAGTCTCTTCACAT
1 TAACTCTTCATCTTCAAGTCTCTTCACAT
1557449 ACCTAGAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.23, C:0.30, G:0.03, T:0.44
Consensus pattern (32 bp):
TAACTCTTCATCTTCAAGTCTCTTCACATTTC
Found at i:1558996 original size:9 final size:9
Alignment explanation
Indices: 1558982--1559006 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1558972 ATGTACACTT
1558982 TATGCCCGA
1 TATGCCCGA
1558991 TATGCCCGA
1 TATGCCCGA
1559000 TATGCCC
1 TATGCCC
1559007 TCGATACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.24
Consensus pattern (9 bp):
TATGCCCGA
Found at i:1559167 original size:20 final size:20
Alignment explanation
Indices: 1559101--1559180 Score: 88
Period size: 20 Copynumber: 3.9 Consensus size: 20
1559091 ACTTTCAGGC
* * * *
1559101 TATGACTCAACATATGTTGC
1 TATGGCTCAACATAGGCTGT
* *
1559121 TATGGCTCAACACAAGAGCTAT
1 TATGGCTCAACA-TAG-GCTGT
1559143 TATGGCTCAACATAGGCTGT
1 TATGGCTCAACATAGGCTGT
1559163 TATGGCTCAACATAGGCT
1 TATGGCTCAACATAGGCT
1559181 ACGTGTTGTG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 33 0.66
21 3 0.06
22 14 0.28
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (20 bp):
TATGGCTCAACATAGGCTGT
Found at i:1565936 original size:33 final size:33
Alignment explanation
Indices: 1565897--1565960 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1565887 TCCGCACAGA
1565897 AGAGATAGTCCACTAGGACAGTAAACACAGAAT
1 AGAGATAGTCCACTAGGACAGTAAACACAGAAT
* * *
1565930 AGAGATAGTCCATTGGGATAGTAAACACAGA
1 AGAGATAGTCCACTAGGACAGTAAACACAGA
1565961 GCTAGTCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (33 bp):
AGAGATAGTCCACTAGGACAGTAAACACAGAAT
Found at i:1573699 original size:30 final size:31
Alignment explanation
Indices: 1573643--1573700 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
1573633 CACTCTTAAA
* *
1573643 ATATTTACACTATTGGTCCTTCAAATTTTTC
1 ATATTTACACTATTAGTCCCTCAAATTTTTC
*
1573674 ATATTTACACT-TTATTCCCTCAAATTT
1 ATATTTACACTATTAGTCCCTCAAATTT
1573701 CGAGTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.28, C:0.21, G:0.03, T:0.48
Consensus pattern (31 bp):
ATATTTACACTATTAGTCCCTCAAATTTTTC
Found at i:1573892 original size:22 final size:22
Alignment explanation
Indices: 1573865--1573906 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1573855 CTTTCTTACT
*
1573865 GTAGTAATTTTCGGGGTATTCA
1 GTAGTAATTTTCGGGATATTCA
1573887 GTAGTAATTTTCGGGATATT
1 GTAGTAATTTTCGGGATATT
1573907 ACATCGTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (22 bp):
GTAGTAATTTTCGGGATATTCA
Found at i:1575786 original size:17 final size:16
Alignment explanation
Indices: 1575740--1575787 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1575730 CTACCTTATG
* **
1575740 ATTAATTAAATCCCTA
1 ATTAATTAATTCGATA
*
1575756 ATTATTTAATTCGATA
1 ATTAATTAATTCGATA
1575772 ATTAATTATATTCGAT
1 ATTAATTA-ATTCGAT
1575788 TGAGTTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTAATTAATTCGATA
Found at i:1583092 original size:29 final size:29
Alignment explanation
Indices: 1583060--1583127 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
1583050 AGTGCGATAT
1583060 AATCGCCAATAACTTATAATATGCAATAA
1 AATCGCCAATAACTTATAATATGCAATAA
1583089 AATCGCCAATAACTTATAATATGCAATAA
1 AATCGCCAATAACTTATAATATGCAATAA
1583118 AATCGCCAAT
1 AATCGCCAAT
1583128 CCCTTCGGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.26
Consensus pattern (29 bp):
AATCGCCAATAACTTATAATATGCAATAA
Found at i:1586663 original size:9 final size:9
Alignment explanation
Indices: 1586649--1586675 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1586639 AAAAAAACCT
1586649 AGTGGCCCA
1 AGTGGCCCA
1586658 AGTGGCCCA
1 AGTGGCCCA
1586667 AGTGGCCCA
1 AGTGGCCCA
1586676 CAACCTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.33, T:0.11
Consensus pattern (9 bp):
AGTGGCCCA
Found at i:1590257 original size:24 final size:25
Alignment explanation
Indices: 1590220--1590272 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
1590210 TCTTTTTGCA
* *
1590220 TTCATTCCATTCATCTGCATTACAT
1 TTCATTACATTCATCTGCATTAAAT
*
1590245 TTCATTACA-TCATTTGCATTAAAT
1 TTCATTACATTCATCTGCATTAAAT
1590269 TTCA
1 TTCA
1590273 CGAAAGAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (25 bp):
TTCATTACATTCATCTGCATTAAAT
Found at i:1590430 original size:11 final size:11
Alignment explanation
Indices: 1590414--1590442 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1590404 TTGCAAAAAG
1590414 AGATGCAAGAC
1 AGATGCAAGAC
1590425 AGATGCAAGAC
1 AGATGCAAGAC
1590436 AGATGCA
1 AGATGCA
1590443 GGAACGACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.17, G:0.28, T:0.10
Consensus pattern (11 bp):
AGATGCAAGAC
Found at i:1593168 original size:20 final size:20
Alignment explanation
Indices: 1593145--1593200 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1593135 AAAATATTTA
*
1593145 AAAAAAAGAGAAAAGAAAGG
1 AAAAAAAGAAAAAAGAAAGG
*
1593165 AAAAGAAGAAAAAAGAAA--
1 AAAAAAAGAAAAAAGAAAGG
* *
1593183 AAAGAAAGAAAGAAGAAA
1 AAAAAAAGAAAAAAGAAA
1593201 AAGAAGAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 15 0.48
20 16 0.52
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAAAGAAAAAAGAAAGG
Found at i:1593185 original size:27 final size:25
Alignment explanation
Indices: 1593146--1593211 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 25
1593136 AAATATTTAA
*
1593146 AAAAAAGAGAAAAGAAAGGAAAAGAAG
1 AAAAAAGAAAAAAGAAA-G-AAAGAAG
1593173 AAAAAAGAAAAAAGAAAGAAAGAAG
1 AAAAAAGAAAAAAGAAAGAAAGAAG
*
1593198 -AAAAAGAAGAAAGA
1 AAAAAAGAAAAAAGA
1593212 GAGGCCAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 13 0.35
25 7 0.19
26 1 0.03
27 16 0.43
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (25 bp):
AAAAAAGAAAAAAGAAAGAAAGAAG
Found at i:1596986 original size:44 final size:43
Alignment explanation
Indices: 1596933--1597155 Score: 189
Period size: 44 Copynumber: 5.0 Consensus size: 43
1596923 AAGATAGCAG
* * *
1596933 ATCTTGCCTTCCTGTACTGACAGTGAAGTAAATCGAAGACACC
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACC
* * * * **
1596976 ATCATTGCCTTCCTGTACTGCCAGC-AGAGTAGATTGAAGATAGAAG
1 ATC-TTGCCTTCCTGTACTGACAGCGA-AGCAGATCGAAG--ACACC
*
1597022 ATCTTGCCTTCCTGTACTGACAACGAAGCAGATCGAAGACACC
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACC
* * * * * * *
1597065 AGCCTTACCTTCTTGTACTGACAGTGAAGCAGA-CTAAAGATAGCAG
1 A-TCTTGCCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACA-C-C
* *
1597111 ATTTTGCCTTCCTGTACTGACAGCGAAGCAAATCGAAGACACC
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACC
1597154 AT
1 AT
1597156 AGTTTGCAGA
Statistics
Matches: 139, Mismatches: 31, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
43 10 0.07
44 61 0.44
45 60 0.43
46 8 0.06
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (43 bp):
ATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACC
Found at i:1597076 original size:89 final size:89
Alignment explanation
Indices: 1596919--1597154 Score: 321
Period size: 89 Copynumber: 2.7 Consensus size: 89
1596909 AGAACAGATC
* * * *
1596919 ACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGTAAATCGAAGACACCATCATTGC
1 ACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAAATCGAAGACACCAGCATTAC
* *
1596984 CTTCCTGTACTGCCAGCAG-AGTAG
66 CTTCCTGTACTGACAG-AGAAGCAG
* * * * *
1597008 ATTGAAGATAGAAGATCTTGCCTTCCTGTACTGACAACGAAGCAGATCGAAGACACCAGCCTTAC
1 ACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAAATCGAAGACACCAGCATTAC
* *
1597073 CTTCTTGTACTGACAGTGAAGCAG
66 CTTCCTGTACTGACAGAGAAGCAG
* *
1597097 ACTAAAGATAGCAGATTTTGCCTTCCTGTACTGACAGCGAAGCAAATCGAAGACACCA
1 ACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAAATCGAAGACACCA
1597155 TAGTTTGCAG
Statistics
Matches: 127, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
88 1 0.01
89 126 0.99
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (89 bp):
ACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAAATCGAAGACACCAGCATTAC
CTTCCTGTACTGACAGAGAAGCAG
Found at i:1597162 original size:45 final size:44
Alignment explanation
Indices: 1596936--1597162 Score: 174
Period size: 45 Copynumber: 5.1 Consensus size: 44
1596926 ATAGCAGATC
* * * ***
1596936 TTGCCTTCCTGTACTGACAGTGAAGTAAATCGAAGACACCATCA
1 TTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAAGT
* * * * *
1596980 TTGCCTTCCTGTACTGCCAGC-AGAGTAGATTGAAGATA-GAAGAT
1 TTGCCTTCCTGTACTGACAGCGA-AGCAGATCGAAGACACCAAG-T
* *
1597024 CTTGCCTTCCTGTACTGACAACGAAGCAGATCGAAGACACC-AGCC
1 -TTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAAG-T
* * * * * * *
1597069 TTACCTTCTTGTACTGACAGTGAAGCAGA-CTAAAGATAGCAGATT
1 TTGCCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACACCA-AGT
*
1597114 TTGCCTTCCTGTACTGACAGCGAAGCAAATCGAAGACACCATAGT
1 TTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCA-AGT
1597159 TTGC
1 TTGC
1597163 AGAAAAGCAG
Statistics
Matches: 139, Mismatches: 35, Indels: 17
0.73 0.18 0.09
Matches are distributed among these distances:
43 3 0.02
44 62 0.45
45 71 0.51
46 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (44 bp):
TTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAAGT
Found at i:1597238 original size:44 final size:45
Alignment explanation
Indices: 1597190--1597481 Score: 221
Period size: 44 Copynumber: 6.6 Consensus size: 45
1597180 AAACCAATCC
* *
1597190 TATCTCCCTGAAGTTGTAGTGGAGTGGATTAA-AACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGTAGATTAAGAACCACAGATCT
* * ** * *
1597234 TATCTCTCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC-CA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGTAGA-TTAAGAACCACAGATCT
*
1597278 TATCTCCCTAAAGTTGCAGTGGAGT-GAATTAA-AACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGTAG-ATTAAGAACCACAGATCT
* * * * * *
1597322 TATCTCTCTGAAGTTGTAGTAGAGTAGA-TCA-CATC-CAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGTAGATTAAGAACCACAGATCT
* ** * *
1597363 TATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAGCCACAAACCT
1 TATCTCCCTGAAGTTGCAGTGGAGTAGA-TTAAGAA-CCACAGATCT
* * * *
1597410 TATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGTAA-CA-AG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGTAGATT-AAG-AACCACAGATCT
*
1597454 TATCTCCCTGAAGTTGTAGTGGAGTAGA
1 TATCTCCCTGAAGTTGCAGTGGAGTAGA
1597482 CAGAAGTTGC
Statistics
Matches: 190, Mismatches: 44, Indels: 28
0.73 0.17 0.11
Matches are distributed among these distances:
41 27 0.14
42 6 0.03
43 10 0.05
44 101 0.53
45 7 0.04
46 7 0.04
47 30 0.16
48 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (45 bp):
TATCTCCCTGAAGTTGCAGTGGAGTAGATTAAGAACCACAGATCT
Found at i:1597309 original size:88 final size:87
Alignment explanation
Indices: 1597180--1597478 Score: 320
Period size: 88 Copynumber: 3.4 Consensus size: 87
1597170 CAGATTAAAT
* *
1597180 AAACCAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGA
1 AAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGAATTAAAACCACAGATCTTATCTCTCTGA
*
1597245 AGTTGCAGTGGAGCAGACAGAAG
66 AGTTGCAGTAGAGCAGAC-GAAG
*
1597268 AAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGTGAATTAAAACCACAGATCTTATCTCTCTGA
1 AAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGAATTAAAACCACAGATCTTATCTCTCTGA
* *
1597333 AGTTGTAGTAGAGTAGATC--A-
66 AGTTGCAGTAGAGCAGA-CGAAG
* * * * * * * *
1597353 CATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA-AAAGAAGCCACAAACCTTATCTCT
1 AAACCAATCCTATCTCCCTGAAGTTGCAGTGGAG-TGA-ATTAA-AA-CCACAGATCTTATCTCT
**
1597417 CTGAAGTTGCAGTAGAGCAGGTTGAAG
62 CTGAAGTTGCAGTAGAGCA-GACGAAG
* * *
1597444 TAA-CAAGTCTTATCTCCCTGAAGTTGTAGTGGAGT
1 AAACCAA-TCCTATCTCCCTGAAGTTGCAGTGGAGT
1597479 AGACAGAAGT
Statistics
Matches: 177, Mismatches: 24, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
85 29 0.16
86 5 0.03
87 3 0.02
88 108 0.61
89 2 0.01
90 3 0.02
91 27 0.15
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (87 bp):
AAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGAATTAAAACCACAGATCTTATCTCTCTGA
AGTTGCAGTAGAGCAGACGAAG
Found at i:1597424 original size:132 final size:132
Alignment explanation
Indices: 1597190--1597481 Score: 330
Period size: 132 Copynumber: 2.2 Consensus size: 132
1597180 AAACCAATCC
* * *
1597190 TATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGTAGTAGAGTAGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTG
* *
1597255 GAGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGTGAATTAAAACCACAGAT
66 GAGCAGACAAAAGAAACCAAACCTATCTCCCTAAAGTTGCAGTGGAGTGAATTAAAACCACAGAT
1597320 CT
131 CT
* * * *
1597322 TATCTCTCTGAAGTTGTAGTAGAGTAGA-TCACATC-CAG-TCTTATCTCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGTAGTAGAGTAGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTG
* * * *
1597384 GAGCAGACAAAAGAAGCCACAAACCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGT--AA
66 GAGCAGACAAAAGAA-AC-CAAACC-TATCTCCCTAAAGTTGCAGT-G-G-A-G-TGAATTAAAA
1597447 -CA-AG-TCT
123 CCACAGATCT
*
1597454 TATCTCCCTGAAGTTGTAGTGGAGTAGA
1 TATCTCCCTGAAGTTGTAGTAGAGTAGA
1597482 CAGAAGTTGC
Statistics
Matches: 137, Mismatches: 15, Indels: 16
0.82 0.09 0.10
Matches are distributed among these distances:
129 37 0.27
130 4 0.03
131 9 0.07
132 72 0.53
133 3 0.02
134 3 0.02
135 3 0.02
136 1 0.01
137 5 0.04
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (132 bp):
TATCTCCCTGAAGTTGTAGTAGAGTAGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTG
GAGCAGACAAAAGAAACCAAACCTATCTCCCTAAAGTTGCAGTGGAGTGAATTAAAACCACAGAT
CT
Found at i:1597488 original size:44 final size:44
Alignment explanation
Indices: 1597231--1597518 Score: 182
Period size: 44 Copynumber: 6.5 Consensus size: 44
1597221 AAACCACAGA
* * *
1597231 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGTAA-CAAG
* * *
1597275 TCCTATCTCCCTAAAGTTGCAGTGGAGT-GA-ATTAA--AACCACAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACA-GAAGTAA-CA-AG
* * * * *
1597318 ATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCA-CA-T--CCAG
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-CAGAAGTAACAAG
* ** *
1597360 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAGCCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGAC---AGAAGTAACAAG
* * * * ***
1597407 CCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGTAACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGTAACAAG
* **
1597451 TCTTATCTCCCTGAAGTTGTAGTGGAGTAGACAGAAGTTGCTAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGTAAC-AAG
*
1597495 TCCTATCTCCCTGAAGTTGCAGTG
1 TCTTATCTCCCTGAAGTTGCAGTG
1597519 CAGCAGATTA
Statistics
Matches: 187, Mismatches: 41, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
40 1 0.01
41 32 0.17
42 4 0.02
43 6 0.03
44 109 0.58
45 5 0.03
47 30 0.16
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGTAACAAG
Done.