Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 17
Found at i:2304994 original size:20 final size:20
Alignment explanation
Indices: 2304969--2305042 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
2304959 AATACAATTA
*
2304969 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
**
2304989 GTGCATCGAAT-CATCAAGGCT
1 GTGCATCG-ATGCATC-CTGCT
*
2305010 GTGCATCGATGTATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
2305030 GTGCATCCATGCA
1 GTGCATCGATGCA
2305043 CGAAGGCTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:2305438 original size:34 final size:32
Alignment explanation
Indices: 2305399--2305468 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2305389 TTTTGTAAAG
* * *
2305399 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
2305433 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2305465 GGGA
1 GGGA
2305469 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2305796 original size:18 final size:18
Alignment explanation
Indices: 2305775--2305817 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2305765 TTTGTCTCGT
2305775 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
2305793 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCGA
2305811 AGGACCA
1 AGGACCA
2305818 TTCCTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.33, G:0.26, T:0.14
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:2307957 original size:21 final size:21
Alignment explanation
Indices: 2307933--2307993 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
2307923 GTAAATCACA
*
2307933 TTGCGATTTTCCGAATTCGTG
1 TTGCGATTTTCCAAATTCGTG
**
2307954 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGTG
*
2307975 ATGCGATTTT-CAAATTCGT
1 TTGCGATTTTCCAAATTCGT
2307994 AACGCGAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 8 0.23
21 27 0.77
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGTG
Found at i:2308000 original size:20 final size:21
Alignment explanation
Indices: 2307956--2308000 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2307946 AATTCGTGTT
*
2307956 GCGATTTTCCAAATTCGCAAT
1 GCGATTTTCCAAATTCGCAAC
*
2307977 GCGATTTT-CAAATTCGTAAC
1 GCGATTTTCCAAATTCGCAAC
2307997 GCGA
1 GCGA
2308001 ATATGTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (21 bp):
GCGATTTTCCAAATTCGCAAC
Found at i:2308017 original size:20 final size:20
Alignment explanation
Indices: 2307994--2308056 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
2307984 TCAAATTCGT
* * *
2307994 AACGCGAATATGTAAATCAC
1 AACGTGAATCTGTAAATCGC
2308014 AACGTGAATCTGTAAATCGC
1 AACGTGAATCTGTAAATCGC
2308034 AACGTGAATCTGTAAATCGC
1 AACGTGAATCTGTAAATCGC
2308054 AAC
1 AAC
2308057 ACAAAAGTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (20 bp):
AACGTGAATCTGTAAATCGC
Found at i:2308111 original size:21 final size:20
Alignment explanation
Indices: 2308064--2308136 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
2308054 AACACAAAAG
2308064 TCAAATTCGCAAAGC-G-ATT
1 TCAAATTCGCAAA-CTGAATT
2308083 TCCAAATTCGCAACACTGAATT
1 T-CAAATTCGCAA-ACTGAATT
*
2308105 TCAAATTCGC-AACTCAATTT
1 TCAAATTCGCAAACTGAA-TT
*
2308125 TCGAATTCGCAA
1 TCAAATTCGCAA
2308137 CAGGTTTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
19 6 0.13
20 24 0.52
21 12 0.26
22 4 0.09
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.29
Consensus pattern (20 bp):
TCAAATTCGCAAACTGAATT
Found at i:2308945 original size:12 final size:12
Alignment explanation
Indices: 2308924--2308957 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2308914 ACCACATTTC
*
2308924 CAATACCAAACA
1 CAATATCAAACA
2308936 CAATATCAAACA
1 CAATATCAAACA
*
2308948 CAATCTCAAA
1 CAATATCAAA
2308958 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:2311743 original size:20 final size:20
Alignment explanation
Indices: 2311718--2311766 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2311708 TGCGATTGTT
2311718 GCGAAAATCAAATTCGAAAC
1 GCGAAAATCAAATTCGAAAC
* * *
2311738 GCGAAAGTAAAATTCGCAAC
1 GCGAAAATCAAATTCGAAAC
2311758 GCGAAAATC
1 GCGAAAATC
2311767 GCAACTCGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.14
Consensus pattern (20 bp):
GCGAAAATCAAATTCGAAAC
Found at i:2313299 original size:21 final size:21
Alignment explanation
Indices: 2313269--2313391 Score: 142
Period size: 21 Copynumber: 5.9 Consensus size: 21
2313259 ATGAATCGGG
* ** *
2313269 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGACAGGGGC
*
2313290 CTCTTTAACGATGACAGGGGC
1 CTCTTGAACGATGACAGGGGC
2313311 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGACAGGGGC
*
2313332 CTCTTGAACGGTGGA-AGGGGC
1 CTCTTGAACGAT-GACAGGGGC
* *
2313353 CTCTTGAACGAT-AGGAGAGGC
1 CTCTTGAACGATGA-CAGGGGC
2313374 CTCTTGAACGATGACAGG
1 CTCTTGAACGATGACAGG
2313392 TGAATCGGGC
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.01
21 83 0.95
22 3 0.03
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.20
Consensus pattern (21 bp):
CTCTTGAACGATGACAGGGGC
Found at i:2313375 original size:63 final size:63
Alignment explanation
Indices: 2313269--2313391 Score: 185
Period size: 63 Copynumber: 2.0 Consensus size: 63
2313259 ATGAATCGGG
* * *
2313269 CTCTTGAACGGTGGGAGGGACCTCTTTAACGATGACAGGGGCCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGAAGGGACCTCTTGAACGATGACAGAGGCCTCTTGAACGATGACAGGGGC
* *
2313332 CTCTTGAACGGTGGAAGGGGCCTCTTGAACGAT-AGGAGAGGCCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGAAGGGACCTCTTGAACGATGA-CAGAGGCCTCTTGAACGATGACAGG
2313392 TGAATCGGGC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 1 0.02
63 53 0.98
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.20
Consensus pattern (63 bp):
CTCTTGAACGGTGGAAGGGACCTCTTGAACGATGACAGAGGCCTCTTGAACGATGACAGGGGC
Found at i:2313692 original size:21 final size:21
Alignment explanation
Indices: 2313668--2313719 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
2313658 TACAACAATC
* * *
2313668 TCACGTAGAGTGGCTACCTCA
1 TCACGTAAAGTAGATACCTCA
2313689 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGTAGATACCTCA
*
2313710 CCACGTAAAG
1 TCACGTAAAG
2313720 CACCATTGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (21 bp):
TCACGTAAAGTAGATACCTCA
Found at i:2314451 original size:20 final size:20
Alignment explanation
Indices: 2314428--2314466 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2314418 ATCGCAACAC
2314428 GATTTTCATTTTCGCGTTGA
1 GATTTTCATTTTCGCGTTGA
*
2314448 GATTTTCATTTTCGTGTTG
1 GATTTTCATTTTCGCGTTG
2314467 CGAATTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.54
Consensus pattern (20 bp):
GATTTTCATTTTCGCGTTGA
Found at i:2314967 original size:19 final size:20
Alignment explanation
Indices: 2314945--2314982 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2314935 AATATTGTGT
2314945 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
2314964 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
2314983 CGCACTTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:2315055 original size:20 final size:20
Alignment explanation
Indices: 2315008--2315057 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
2314998 TGACTTCTGT
* *
2315008 GTTGCGAATTACAGATTCGC
1 GTTGCGATTTACAGATCCGC
2315028 GTTGCGATTTACAGATCCGC
1 GTTGCGATTTACAGATCCGC
2315048 GTTGCGATTT
1 GTTGCGATTT
2315058 TATTGGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAGATCCGC
Found at i:2319542 original size:12 final size:12
Alignment explanation
Indices: 2319525--2319551 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2319515 TAATGGAACA
2319525 TTTTCTTCTTCT
1 TTTTCTTCTTCT
2319537 TTTTCTTCTTCT
1 TTTTCTTCTTCT
2319549 TTT
1 TTT
2319552 CAGCAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTCTTCT
Found at i:2320900 original size:170 final size:171
Alignment explanation
Indices: 2320618--2320959 Score: 677
Period size: 170 Copynumber: 2.0 Consensus size: 171
2320608 GACGTTGTTG
2320618 AAGATGACGAGGGTGCAAATAGTCCAAACCAGAAAGGTGTTACCCAATTAGAAAGTGAACGGTTC
1 AAGATGACGAGGGTGCAAATAGTCCAAACCAGAAAGGTGTTACCCAATTAGAAAGTGAACGGTTC
2320683 ATTACAAACTCATCAAGAGCTTTGGACCAAGATGCTGGAAGATATGAGGGTGAGAATTCTCGGCA
66 ATTACAAACTCATCAAGAGCTTTGGACCAAGATGCTGGAAGATATGAGGGTGAGAATTCTCGGCA
2320748 AACTAGCTC-TTATCATGTCAGGTCATTCCACAGCATAAAA
131 AACTAGCTCTTTATCATGTCAGGTCATTCCACAGCATAAAA
2320788 AAGATGACGAGGGTGCAAATAGTCCAAACCAGAAAGGTGTTACCCAATTAGAAAGTGAACGGTTC
1 AAGATGACGAGGGTGCAAATAGTCCAAACCAGAAAGGTGTTACCCAATTAGAAAGTGAACGGTTC
2320853 ATTACAAACTCATCAAGAGCTTTGGACCAAGATGCTGGAAGATATGAGGGTGAGAATTCTCGGCA
66 ATTACAAACTCATCAAGAGCTTTGGACCAAGATGCTGGAAGATATGAGGGTGAGAATTCTCGGCA
2320918 AACTAGCTCTTTATCATGTCAGGTCATTCCACAGCATAAAA
131 AACTAGCTCTTTATCATGTCAGGTCATTCCACAGCATAAAA
2320959 A
1 A
2320960 GTATTGGAGC
Statistics
Matches: 171, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
170 139 0.81
171 32 0.19
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (171 bp):
AAGATGACGAGGGTGCAAATAGTCCAAACCAGAAAGGTGTTACCCAATTAGAAAGTGAACGGTTC
ATTACAAACTCATCAAGAGCTTTGGACCAAGATGCTGGAAGATATGAGGGTGAGAATTCTCGGCA
AACTAGCTCTTTATCATGTCAGGTCATTCCACAGCATAAAA
Found at i:2328628 original size:35 final size:35
Alignment explanation
Indices: 2328582--2328652 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
2328572 CAGACTCCAT
2328582 TGCCAAAACTTTATCTTCCATCTTCTCAAAAGATG
1 TGCCAAAACTTTATCTTCCATCTTCTCAAAAGATG
2328617 TGCCAAAACTTTATCTTCCATCTTCTCAAAAGATG
1 TGCCAAAACTTTATCTTCCATCTTCTCAAAAGATG
2328652 T
1 T
2328653 TAAAACACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.35
Consensus pattern (35 bp):
TGCCAAAACTTTATCTTCCATCTTCTCAAAAGATG
Found at i:2329133 original size:10 final size:10
Alignment explanation
Indices: 2329105--2329160 Score: 71
Period size: 10 Copynumber: 5.7 Consensus size: 10
2329095 TGGCCCTGCA
*
2329105 AAATAA-AAA
1 AAATAATAAT
*
2329114 AAATATTAAT
1 AAATAATAAT
2329124 AAATAATAAT
1 AAATAATAAT
2329134 -AATAATAAAT
1 AAATAAT-AAT
2329144 AAATAATAAT
1 AAATAATAAT
2329154 AAATAAT
1 AAATAAT
2329161 TTTTTTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
9 11 0.27
10 24 0.59
11 6 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATAATAAT
Found at i:2329669 original size:168 final size:162
Alignment explanation
Indices: 2329419--2329985 Score: 555
Period size: 168 Copynumber: 3.5 Consensus size: 162
2329409 TGACATATAG
* * * * * *
2329419 CCCTTCTCGTCTTGAGTTATGTTGTAAATTTGATTTGCCTCTG-AGTTGAATGTAATCGAACTCG
1 CCCTTCTAGCCTTGAGTTATGTTGCAAA--TGATGTGCCT-TGAAGCTGAGTGTAATCGAACTCG
* *
2329483 AAGGA-CTTTGGTTGGCAGATAGCCCTTCTCACCTTAAGCTATAATGAAAATGATGTGCCTTGGA
63 AAGGATCTTTGGTTGGCAGATAGCCCTTCT-ACCTTAAGCTATGATGAAAATGATGTGCCTTTGA
* * * *
2329547 GCTGAGAGTATTCGAACTCGAAGGTCTTTTGTTGGCAAATAG
127 GCTGA-AG-AATCGAACTCTAAGGTC---T-TTGGCAGATAA
* * * * *
2329589 CCCTTCTTGCCTTGAGCTATGTTGCAAGTGATGTGCCTT-AGAGCTGAGCGTAGTCGAACTCGAA
1 CCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTGA-AGCTGAGTGTAATCGAACTCGAA
* * * * * *
2329653 -GATCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCTTTGAGC
65 GGATCTTTGGTTGGCAGATAGCCCTTCTA-CCTTAAGCTATGATGAAAATGATGTGCCTTTGAGC
2329717 TGAATGGAATCGAACTCTAAGGTCTTTGGCAGATAA
129 TGAA--GAATCGAACTCTAAGGTCTTTGGCAGATAA
*
2329753 CCCTTCTAGCCTTGAGTTAT-TCTGCAAATGATGTGCCCTTGAAGCTAAGTGTAATCGAACTCG-
1 CCCTTCTAGCCTTGAGTTATGT-TGCAAATGATGTG-CCTTGAAGCTGAGTGTAATCGAACTCGA
* * * * * **
2329816 AGGGTC--T--TTGGCAGATAGCTCTTCTTGCCTTAAGCTATGCTGCAAATGATGCACCTTTGAG
64 AGGATCTTTGGTTGGCAGATAGCCCTTC-TACCTTAAGCTATGATGAAAATGATGTGCCTTTGAG
2329877 CTGAATAGAATCGAACTCTAAGGTCTTT-GCAGATAA
128 CTG-A-AGAATCGAACTCTAAGGTCTTTGGCAGATAA
* * *
2329913 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCGAACTCGAA
1 CCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTG-CCTTGAAGCTGAGTGTAATCGAACTCGAA
*
2329978 TG-TCTTTG
65 GGATCTTTG
2329986 TGTTTCAAGA
Statistics
Matches: 335, Mismatches: 44, Indels: 43
0.79 0.10 0.10
Matches are distributed among these distances:
160 68 0.20
161 68 0.20
162 3 0.01
163 3 0.01
164 40 0.12
165 26 0.08
166 1 0.00
167 5 0.01
168 97 0.29
169 1 0.00
170 23 0.07
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (162 bp):
CCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTGAAGCTGAGTGTAATCGAACTCGAAG
GATCTTTGGTTGGCAGATAGCCCTTCTACCTTAAGCTATGATGAAAATGATGTGCCTTTGAGCTG
AAGAATCGAACTCTAAGGTCTTTGGCAGATAA
Found at i:2329782 original size:80 final size:80
Alignment explanation
Indices: 2329449--2329985 Score: 458
Period size: 84 Copynumber: 6.5 Consensus size: 80
2329439 GTTGTAAATT
* * * * *
2329449 TGATTTGCCTCTGAGTTGAATGTAATCGAACTCGAAGGACTTTGGTTGGCAGATAGCCCTTCTCA
1 TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGG--TCT--TTGGCAGATAACCCTTCT-A
* ** *
2329514 -CCTTAAGCTATAATGAAAA
61 GCCTTGAGCTATTCTGCAAA
* * * * *
2329533 TGATGTGCCTTGGAGCTGAGA-GTATTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTT
1 TGATGTGCCTTTGAGCTGA-ATGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTA
*
2329597 GCCTTGAGCTATGT-TGCAAG
61 GCCTTGAGCTAT-TCTGCAAA
* ** * *
2329617 TGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTTGGCAGATAACCCTTCTAG
1 TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTAG
* *
2329682 CCTTGAGTTATGT-TGTAAA
62 CCTTGAGCTAT-TCTGCAAA
* * *
2329701 TGATATGCCTTTGAGCTGAATGGAATCGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTT
1 TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTT
*
2329766 GAGTTATTCTGCAAA
66 GAGCTATTCTGCAAA
* * * * *
2329781 TGATGTGCCCTTGAAGCT-AAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCTCTTCTTGCC
1 TGATGTGCCTTTG-AGCTGAA-TGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCC
* *
2329845 TTAAGCTATGCTGCAAA
64 TTGAGCTATTCTGCAAA
** *
2329862 TGATGCACCTTTGAGCTGAATAG-AATCGAACTCTAAGGTCTTT-GCAGATAACCCTTCTAGCCT
1 TGATGTGCCTTTGAGCTGAAT-GTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCT
* *
2329925 TGAGTTATGCTGCAAA
65 TGAGCTATTCTGCAAA
* * * * *
2329941 TGATGTGCCCTCGAAGCTGAGTGTAGTCGAACTCGAATGTCTTTG
1 TGATGTGCCTTTG-AGCTGAATGTAATCGAACTCGAAGGTCTTTG
2329986 TGTTTCAAGA
Statistics
Matches: 377, Mismatches: 60, Indels: 35
0.80 0.13 0.07
Matches are distributed among these distances:
79 42 0.11
80 96 0.25
81 68 0.18
82 2 0.01
83 3 0.01
84 164 0.44
85 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (80 bp):
TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTT
GAGCTATTCTGCAAA
Found at i:2329973 original size:160 final size:161
Alignment explanation
Indices: 2329494--2329985 Score: 560
Period size: 160 Copynumber: 3.0 Consensus size: 161
2329484 AGGACTTTGG
* * *
2329494 TTGGCAGATAGCCCTTCTCA-CCTTAAGCTATAATGAAAATGATGTGCCTTGGAGCTG-AGAGTA
1 TTGGCAGATAGCCCTTCT-AGCCTTAAGCTATGATGAAAATGATGTGCCTTTGAGCTGAATAG-A
* * * * * * * *
2329557 TTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAGTGATG
64 ATCGAACTCTAAGGTC---T-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
* * *
2329622 TGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGATCTTT
125 TGCCCTAGAAGCTGAGTGTAGTCGAACTCGAAGGTC--T
* * * * * * *
2329660 GGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCTTTGAGCTGAATGGA
1 --TTGGCAGATAGCCCTTCTAGCCTTAAGCTATGATGAAAATGATGTGCCTTTGAGCTGAATAGA
*
2329725 ATCGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATTCTGCAAATGATGTGCC
64 ATCGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC
* * * *
2329790 CTTGAAGCTAAGTGTAATCGAACTCGAGGGTCT
129 CTAGAAGCTGAGTGTAGTCGAACTCGAAGGTCT
* * * * **
2329823 TTGGCAGATAGCTCTTCTTGCCTTAAGCTATGCTGCAAATGATGCACCTTTGAGCTGAATAGAAT
1 TTGGCAGATAGCCCTTCTAGCCTTAAGCTATGATGAAAATGATGTGCCTTTGAGCTGAATAGAAT
2329888 CGAACTCTAAGGTCTTT-GCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
66 CGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
* *
2329952 CGAAGCTGAGTGTAGTCGAACTCGAATGTCT
131 AGAAGCTGAGTGTAGTCGAACTCGAAGGTCT
2329983 TTG
1 TTG
2329986 TGTTTCAAGA
Statistics
Matches: 278, Mismatches: 43, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
160 75 0.27
161 71 0.26
163 1 0.00
164 43 0.15
165 23 0.08
167 1 0.00
168 62 0.22
169 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (161 bp):
TTGGCAGATAGCCCTTCTAGCCTTAAGCTATGATGAAAATGATGTGCCTTTGAGCTGAATAGAAT
CGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
AGAAGCTGAGTGTAGTCGAACTCGAAGGTCT
Found at i:2330060 original size:33 final size:34
Alignment explanation
Indices: 2330018--2330094 Score: 129
Period size: 34 Copynumber: 2.3 Consensus size: 34
2330008 GGTTTTTTTC
*
2330018 CAAGAGAAACGATTTC-AAGTTTTTTTTATGTTT
1 CAAGAGAAACGATTTCAAAGGTTTTTTTATGTTT
*
2330051 CAAGAGAAACGATTTCAAAGGTTTTTTTGTGTTT
1 CAAGAGAAACGATTTCAAAGGTTTTTTTATGTTT
2330085 CAAGAGAAAC
1 CAAGAGAAAC
2330095 TGTCTCCAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 16 0.39
34 25 0.61
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (34 bp):
CAAGAGAAACGATTTCAAAGGTTTTTTTATGTTT
Found at i:2330130 original size:71 final size:67
Alignment explanation
Indices: 2330048--2330385 Score: 192
Period size: 67 Copynumber: 5.0 Consensus size: 67
2330038 TTTTTTTATG
* * *
2330048 TTTCAAGAGAAACGAT-TTCAAAGGTTTTTTTGTGTTTCAAGAGAAACTGTCTCCAGGGAGACAA
1 TTTCAAGAGAAA-GATATTCAAAGG----TTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
*
2330112 AATTTTA
61 AACTTTA
* *
2330119 TTTCAAGAGAAATATATTCAAAGGTTGGTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TTTCAAGAGAAAGATATTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
*
2330184 TG
66 TA
* * * **** * * *
2330186 TTTCAAGGGAAA-TTGTCTCAAGAGAGACAAAACTTATTTCTAA-AGAAACAGTCTCAAGGGAGA
1 TTTCAAGAGAAAGATAT-TCAA-AG-G----TTGGTGTTTC-AAGAGAAACTGTCTCAAGAGAGA
* *
2330249 CGAAA-TTTG
58 CAAAACTTTA
* * * * *
2330258 TTTCAAG-GAAAACATATTCAAAGATT-TTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAA-T
1 TTTCAAGAG-AAAGATATTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
*
2330320 TTG
65 TTA
* * * ** * *
2330323 TTTCAAGAGAGACAAAGACAAA-ATT--TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TTTCAAGAGAAAGATATTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
2330385 T
66 T
2330386 GTTCCAAAAT
Statistics
Matches: 217, Mismatches: 36, Indels: 35
0.75 0.12 0.12
Matches are distributed among these distances:
63 31 0.14
64 8 0.04
65 47 0.22
66 3 0.01
67 52 0.24
68 2 0.01
69 1 0.00
70 2 0.01
71 23 0.11
72 18 0.08
73 28 0.13
74 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (67 bp):
TTTCAAGAGAAAGATATTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
TA
Found at i:2330249 original size:36 final size:37
Alignment explanation
Indices: 2330149--2330268 Score: 122
Period size: 37 Copynumber: 3.3 Consensus size: 37
2330139 AAGGTTGGTG
** *
2330149 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAGAGAAACAGTCTCAAGAGAGACAAAACTTTA
* **
2330186 TTTCAAGGGAAATTGTCTCAAGAGAGACAAAAC-TTA
1 TTTCAAGAGAAACAGTCTCAAGAGAGACAAAACTTTA
* * *
2330222 TTTCTAA-AGAAACAGTCTCAAGGGAGACGAAA-TTTG
1 TTTC-AAGAGAAACAGTCTCAAGAGAGACAAAACTTTA
2330258 TTTCAAG-GAAA
1 TTTCAAGAGAAA
2330269 ACATATTCAA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
35 6 0.08
36 32 0.44
37 34 0.47
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (37 bp):
TTTCAAGAGAAACAGTCTCAAGAGAGACAAAACTTTA
Found at i:2330271 original size:36 final size:35
Alignment explanation
Indices: 2330147--2330554 Score: 177
Period size: 36 Copynumber: 11.9 Consensus size: 35
2330137 CAAAGGTTGG
**
2330147 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAG-GAAACAGTCTCAAGAGAGACAAAA-TT
** *
2330184 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAACT
1 TGTTTCAA-GGAAACAGTCTCAAGAGAGACAAAATT
* * * *
2330220 TATTTCTAAAGAAACAGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGGAAACAGTCTCAAGAGAGACAAAATT
* *
2330256 TGTTTCAAGGAAAACA-TATTC-A-A-AG----ATTT
1 TGTTTCAAGG-AAACAGT-CTCAAGAGAGACAAAATT
*
2330285 TGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATT
1 TGTTTCAA-GGAAACAGTCTCAAGAGAGACAAAATT
* *
2330321 TGTTTCAA-G--AGAG--AC-A-A-AGACAAAATT
1 TGTTTCAAGGAAACAGTCTCAAGAGAGACAAAATT
**
2330348 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAG-GAAACAGTCTCAAGAGAGACAAAA-TT
* ** ** *
2330385 TGTTCCAAAATAAATTGTCTCAAGGGAGACAAAATT
1 TGTTTC-AAGGAAACAGTCTCAAGAGAGACAAAATT
* * *
2330421 TGTTT-AATGTAAA-AGATATTC-A-A-AG----ATTT
1 TGTTTCAA-GGAAACAG-T-CTCAAGAGAGACAAAATT
2330450 TGTTTCAAGGGAAACTA-TCTCAAGAGAGACAAAATT
1 TGTTTCAA-GGAAAC-AGTCTCAAGAGAGACAAAATT
*
2330486 TGTTTCAAGAGAAACTA-TCTGAAGAGAGACAAAATTT
1 TGTTTCAAG-GAAAC-AGTCTCAAGAGAGACAAAA-TT
** * * *
2330523 TGTTTTGAGTAAATTAGTCTCAAGCGAGACAA
1 TGTTTCAAGGAAA-CAGTCTCAAGAGAGACAA
2330555 CCCCTTGTTT
Statistics
Matches: 287, Mismatches: 43, Indels: 82
0.70 0.10 0.20
Matches are distributed among these distances:
27 18 0.06
28 1 0.00
29 29 0.10
30 13 0.05
31 4 0.01
32 7 0.02
33 5 0.02
34 5 0.02
35 13 0.05
36 104 0.36
37 85 0.30
38 3 0.01
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGGAAACAGTCTCAAGAGAGACAAAATT
Found at i:2330372 original size:42 final size:37
Alignment explanation
Indices: 2330338--2330424 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
2330328 AGAGAGACAA
* *
2330338 AGACAAAA-TTTGTTTCAAGAGAAATTGTCTCAAGAG
1 AGACAAAACTTTGTTCCAAAAGAAATTGTCTCAAGAG
* *
2330374 AGACAAAACTTTGTTCCAAAATAAATTGTCTCAAGGG
1 AGACAAAACTTTGTTCCAAAAGAAATTGTCTCAAGAG
2330411 AGACAAAA-TTTGTT
1 AGACAAAACTTTGTT
2330425 TAATGTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 14 0.30
37 32 0.70
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (37 bp):
AGACAAAACTTTGTTCCAAAAGAAATTGTCTCAAGAG
Found at i:2330376 original size:65 final size:63
Alignment explanation
Indices: 2330210--2330388 Score: 191
Period size: 65 Copynumber: 2.8 Consensus size: 63
2330200 GTCTCAAGAG
* * * * *
2330210 AGACAAAACTTATTTCTAA-AGAAACAGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAACAT
1 AGACAAAATTTGTTTC-AAGAGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAA
** * * *
2330273 ATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTCAA-GAGAGACA
1 AGACAAA-A-TTTGTTTCAAGAGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGA-AAACA
2330337 A
63 A
**
2330338 AGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTT
1 AGACAAAATTTGTTTCAAGAGAAACAGTCTCAAGAGAGACAAAA-TTTGTT
2330389 CCAAAATAAA
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
63 38 0.40
64 12 0.12
65 46 0.48
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (63 bp):
AGACAAAATTTGTTTCAAGAGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAA
Found at i:2330442 original size:165 final size:165
Alignment explanation
Indices: 2330173--2330497 Score: 512
Period size: 165 Copynumber: 2.0 Consensus size: 165
2330163 GTCTCAAGAG
* *
2330173 AGACAAAACTTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAACTTATTTCTAAAGAAACAGT
1 AGACAAAACTTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTATTTCAAAAGAAACAGT
* *
2330238 CTCAAGGGAGACGAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACCGT
66 CTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACCAT
2330303 CTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAA
131 CTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAA
* **
2330338 AGACAAAA-TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT-TGTTCCAAAATAAATT
1 AGACAAAACTTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAT-TT-CAAAAGAAACA
* *
2330401 GTCTCAAGGGAGACAAAATTTGTTT-AATGTAAAAGATATTCAAAGATTTTGTTTCAAGGGAAAC
64 GTCTCAAGGGAGACAAAATTTGTTTCAA-GGAAAACATATTCAAAGATTTTGTTTCAAGGGAAAC
*
2330465 TATCTCAAGAGAGACAAAATTTGTTTCAAGAGA
128 CATCTCAAGAGAGACAAAATTTGTTTCAAGAGA
2330498 AACTATCTGA
Statistics
Matches: 147, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
163 1 0.01
164 42 0.29
165 104 0.71
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (165 bp):
AGACAAAACTTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTATTTCAAAAGAAACAGT
CTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACCAT
CTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAA
Found at i:2331179 original size:124 final size:123
Alignment explanation
Indices: 2330716--2331181 Score: 601
Period size: 124 Copynumber: 3.8 Consensus size: 123
2330706 GGCACAATAA
* * ** * * ***
2330716 CCTTCTTCGTGAAGTTGAAATCGTGGATGGGTCATTCGTTGTGAAATTGAGCTTTTAATTGGGCA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGC-CTTAATTGAATA
* * * * * * **
2330781 TCCTTCGTCGGGAAGTTGAAATCCAACCTGAAGATGAATGTTGCTGGTGGGTATAATTC
65 TCATTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTGGTGAGCACGATTC
* * * *
2330840 CCTTCGTCGTGAAGTTGAAACCGTTGATGGCCTC-TTCGTTATGAAGTTGAGTCTTGAATTGGAT
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCC-CATTCGTTGTGAAGTTGAGCCTT-AATTGAAT
* * * *
2330904 ATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTC
64 ATCATTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTGGTGAGCACGATTC
*
2330964 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTTGTTGTGAAGTTGAGCCTTAACTTGAATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAA-TTGAATA
* **
2331029 TCATTCATCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTAATGAGCACGATTC
65 TCATTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTGGTGAGCACGATTC
* *
2331088 CCTTCGTCGTGAAGTTGAAACTGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTAACTTGAATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAA-TTGAATA
2331153 TCATTCGTCGTGAAGTTGAAATCCAAGCT
65 TCATTCGTCGTGAAGTTGAAATCCAAGCT
2331182 TGTATTGTTT
Statistics
Matches: 302, Mismatches: 36, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
123 5 0.02
124 296 0.98
125 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (123 bp):
CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAATTGAATAT
CATTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTGGTGAGCACGATTC
Found at i:2339654 original size:30 final size:32
Alignment explanation
Indices: 2339620--2339689 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 32
2339610 ATATATATAT
2339620 ATATAATATTAATAA-ATTTA-ATTTAAATT-A
1 ATATAATATT-ATAATATTTATATTTAAATTAA
*
2339650 ATAT-ATA-TATAATATTTATATTTAATTTAA
1 ATATAATATTATAATATTTATATTTAAATTAA
2339680 ATATATATAT
1 ATATA-ATAT
2339690 ATGCGGCCCG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
27 4 0.12
28 6 0.18
29 11 0.33
30 9 0.27
32 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
ATATAATATTATAATATTTATATTTAAATTAA
Found at i:2339661 original size:36 final size:32
Alignment explanation
Indices: 2339612--2339691 Score: 115
Period size: 36 Copynumber: 2.4 Consensus size: 32
2339602 TATTATATAT
2339612 ATATATATATATAATATTAATAAATTTAATTTAA
1 ATATATATATATAATATT--TAAATTTAATTTAA
*
2339646 ATTAATATATATATAATATTTATATTTAATTTAA
1 A-T-ATATATATATAATATTTAAATTTAATTTAA
2339680 ATATATATATAT
1 ATATATATATAT
2339692 GCGGCCCGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
32 10 0.23
33 1 0.02
34 15 0.35
35 1 0.02
36 16 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
ATATATATATATAATATTTAAATTTAATTTAA
Found at i:2339690 original size:30 final size:27
Alignment explanation
Indices: 2339623--2339690 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 27
2339613 TATATATATA
2339623 TAATAT-TA-ATAAATTTAATTTAAAT
1 TAATATATATATAAATTTAATTTAAAT
*
2339648 TAATATATATATAATATTTATATTTAATT
1 TAATATATATATAA-ATTTA-ATTTAAAT
2339677 TAAATATATATATA
1 T-AATATATATATA
2339691 TGCGGCCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 6 0.16
26 2 0.05
27 4 0.11
28 5 0.14
29 8 0.22
30 12 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TAATATATATATAAATTTAATTTAAAT
Found at i:2342632 original size:16 final size:16
Alignment explanation
Indices: 2342611--2342644 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2342601 CACGTGTCAA
2342611 TTTTGTATGCCTTTAG
1 TTTTGTATGCCTTTAG
2342627 TTTTGTATGCCTTTAG
1 TTTTGTATGCCTTTAG
2342643 TT
1 TT
2342645 AGGTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (16 bp):
TTTTGTATGCCTTTAG
Found at i:2346176 original size:345 final size:343
Alignment explanation
Indices: 2345530--2346220 Score: 1214
Period size: 345 Copynumber: 2.0 Consensus size: 343
2345520 AATAAAGAAG
*
2345530 AATTTTGATGTCCACAAATGTGAGGAGATGAGAGTTGGGCATGTGTTTTTGTGAATCAATTTGGT
1 AATTTTGATGCCCACAAA-GTGAGGAGATGAGAGTTGGGCATGTG-TTTTGTGAATCAATTTGGT
2345595 GGCTTAAAATGATCCAACCCCACATGCTAAATCCTCAAGAGAAAAAGTGCAAAAAGTGGGCAGTT
64 GGCTTAAAATGATCCAACCCCACATGCTAAATCCTCAAGAGAAAAAGTGCAAAAAGTGGGCAGTT
2345660 TTGGATTGGATGAACAAGTATATAGGCCATGGAAGTGCACTTTTTGGCTTCTCAACTTCAAGGCA
129 TTGGATTGGATGAACAAGTATATAGGCCATGGAAGTGCACTTTTTGGCTTCTCAACTTCAAGGCA
2345725 ATGAAGTCATCATACCAACAATGAAGTGAAGAGTTTTCTTCTTCATATTTCTTTCTTTTTTCAAA
194 ATGAAGTCATCATACCAACAATGAAGTGAAGAGTTTTCTTCTTCATATTTCTTTCTTTTTTCAAA
* *
2345790 GAATTTTGAAGTGTAAATTCGATTTATATTTGTTTTTTATTCTATATGAAGAATGT-AA-TTGTG
259 GAATTTTGAAGCGTAAATTCGATTTATATTTGTTGTTTATTCTATATGAAGAATGTAAATTTGTG
*
2345853 T-TGCAATATTGATCGTAGT
324 TGTGCAATATTGATCATAGT
2345872 AATTTTGATGCCCACAAA-TGAGGAGATGAGAGTTGGGCATGTG-TTTGTGAATCAATTTGGTGG
1 AATTTTGATGCCCACAAAGTGAGGAGATGAGAGTTGGGCATGTGTTTTGTGAATCAATTTGGTGG
2345935 CTTAAAATGATCCAAACCCCACATGCTAAATCCTCAAGAGAGAAAAAGTGCAAAAAGTGGGCAGT
66 CTTAAAATGATCC-AACCCCACATGCTAAATCCTC-A-AGAGAAAAAGTGCAAAAAGTGGGCAGT
2346000 TTTGGATTGGATGAACAAGTATATAGGCCATGGAGAAGTGCACTTTTTGGCTTCTCAACTTCAAG
128 TTTGGATTGGATGAACAAGTATATAGGCCAT-G-GAAGTGCACTTTTTGGCTTCTCAACTTCAAG
2346065 GCAATGAAGTCATCATACCAACAATGAAGAGTGAAGAG-TTTCTTCTTCATATTTCTTTCTTTTT
191 GCAATGAAGTCATCATACCAACAATG-A-AGTGAAGAGTTTTCTTCTTCATATTTCTTTC-TTTT
2346129 TTCAAAGAATTTTGAAGCGTAAATTCGATTTATATTTGTTGTTTATTCTATATGAAGAATGTAAA
253 TTCAAAGAATTTTGAAGCGTAAATTCGATTTATATTTGTTGTTTATTCTATATGAAGAATGTAAA
2346194 TTTGTGTGTGCAATATTGATCATAGT
318 TTTGTGTGTGCAATATTGATCATAGT
2346220 A
1 A
2346221 TAGAGAATGT
Statistics
Matches: 334, Mismatches: 4, Indels: 16
0.94 0.01 0.05
Matches are distributed among these distances:
338 33 0.10
339 21 0.06
340 26 0.08
341 58 0.17
342 18 0.05
343 57 0.17
344 22 0.07
345 73 0.22
346 2 0.01
347 6 0.02
348 18 0.05
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (343 bp):
AATTTTGATGCCCACAAAGTGAGGAGATGAGAGTTGGGCATGTGTTTTGTGAATCAATTTGGTGG
CTTAAAATGATCCAACCCCACATGCTAAATCCTCAAGAGAAAAAGTGCAAAAAGTGGGCAGTTTT
GGATTGGATGAACAAGTATATAGGCCATGGAAGTGCACTTTTTGGCTTCTCAACTTCAAGGCAAT
GAAGTCATCATACCAACAATGAAGTGAAGAGTTTTCTTCTTCATATTTCTTTCTTTTTTCAAAGA
ATTTTGAAGCGTAAATTCGATTTATATTTGTTGTTTATTCTATATGAAGAATGTAAATTTGTGTG
TGCAATATTGATCATAGT
Found at i:2357423 original size:120 final size:121
Alignment explanation
Indices: 2357254--2357471 Score: 375
Period size: 120 Copynumber: 1.8 Consensus size: 121
2357244 ATATAACATA
* * **
2357254 ATTTCTGTCATTGTAATCACGTAACTTGATTTTTATTCGTCTTGTTTAGACAAATAATGAAAGAA
1 ATTTCTGTCATTGTAATCACGTAACTCGATTTTCATTCGTCTTGTTTAGACAAATAACCAAAGAA
2357319 ATAGAGAAATATAAATGTAAAAAAAATATTTAGTTTTTCTTTCTTTCAAATCTGCC
66 ATAGAGAAATATAAATGTAAAAAAAATATTTAGTTTTTCTTTCTTTCAAATCTGCC
*
2357375 ATTTTTGTCATTGTAATCACG-AACTCGATTTTCATTCGTCTTGTTTAGACAAATAACCAAAGAA
1 ATTTCTGTCATTGTAATCACGTAACTCGATTTTCATTCGTCTTGTTTAGACAAATAACCAAAGAA
*
2357439 ATAGAGAAATATAAATGTAAAAAAATTATTTAG
66 ATAGAGAAATATAAATGTAAAAAAAATATTTAG
2357472 GGGCTTATTT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
120 71 0.78
121 20 0.22
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (121 bp):
ATTTCTGTCATTGTAATCACGTAACTCGATTTTCATTCGTCTTGTTTAGACAAATAACCAAAGAA
ATAGAGAAATATAAATGTAAAAAAAATATTTAGTTTTTCTTTCTTTCAAATCTGCC
Found at i:2357927 original size:35 final size:35
Alignment explanation
Indices: 2357881--2357953 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
2357871 GTGACACGTG
*
2357881 TCATATTTATATTTTGACTTAATGTAAAAAAGCAC
1 TCATATTTATATTTTGACTTAATGTAAAAAAACAC
*
2357916 TCATATTTATATTTTGTCTTAATGTAAAAAAACAC
1 TCATATTTATATTTTGACTTAATGTAAAAAAACAC
2357951 TCA
1 TCA
2357954 AACTATACTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (35 bp):
TCATATTTATATTTTGACTTAATGTAAAAAAACAC
Found at i:2360070 original size:46 final size:46
Alignment explanation
Indices: 2360000--2360105 Score: 160
Period size: 46 Copynumber: 2.3 Consensus size: 46
2359990 TACACAAAGG
* *
2360000 GTGCATCGATGCATAAAATACATTCGATGTTTTAA-ACAAGCCTGGA
1 GTGCATCGATGCATAAAATACATTCGATGTTTCAATAAAAGCCT-GA
* *
2360046 GTGCATCGATGCATAAAATGCATTCGATGTTTCAATAAAATCCTGA
1 GTGCATCGATGCATAAAATACATTCGATGTTTCAATAAAAGCCTGA
2360092 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2360106 GACTATGCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
46 49 0.89
47 6 0.11
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATACATTCGATGTTTCAATAAAAGCCTGA
Found at i:2362258 original size:32 final size:32
Alignment explanation
Indices: 2362190--2362277 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
2362180 GTAAACTATT
* *
2362190 CATATGTTCCTTAGAACATAGGT-ATATTGTC
1 CATATGTTCCGTAAAACATAGGTAATATTGTC
2362221 CATATG-TCTCG-AAAGACATAGGTAAT-TCTGTC
1 CATATGTTC-CGTAAA-ACATAGGTAATAT-TGTC
2362253 CATATGTTCCGTAAAACATAGGTAA
1 CATATGTTCCGTAAAACATAGGTAA
2362278 ACCCTCGACT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
30 4 0.08
31 16 0.33
32 24 0.49
33 5 0.10
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (32 bp):
CATATGTTCCGTAAAACATAGGTAATATTGTC
Found at i:2362499 original size:28 final size:26
Alignment explanation
Indices: 2362436--2362501 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
2362426 ACATATACCT
2362436 TTTCTCATATTCATATAATCATATCA
1 TTTCTCATATTCATATAATCATATCA
* * *
2362462 TTTCATTCATATTCGTATATCTCATGTTCA
1 TTTC--TCATATTCATATA-ATCAT-ATCA
2362492 TTTCTCATAT
1 TTTCTCATAT
2362502 AGTCACATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 4 0.12
28 18 0.55
29 4 0.12
30 7 0.21
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.50
Consensus pattern (26 bp):
TTTCTCATATTCATATAATCATATCA
Found at i:2362686 original size:16 final size:16
Alignment explanation
Indices: 2362665--2362702 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2362655 ATGTCACCTC
*
2362665 TCATATGATTTCATA-T
1 TCATATGATAT-ATATT
2362681 TCATATGATATATATT
1 TCATATGATATATATT
2362697 TCATAT
1 TCATAT
2362703 TTTTTTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (16 bp):
TCATATGATATATATT
Found at i:2367005 original size:32 final size:32
Alignment explanation
Indices: 2366924--2367024 Score: 102
Period size: 31 Copynumber: 3.2 Consensus size: 32
2366914 CCAAAGAATC
* * * *
2366924 TAGGTAA-ACTATCCATATATTCCTTAGAACA
1 TAGGTAATACTGTCCATATGTTCCGTAAAACA
2366955 TAGGT-ATACTGTCCATATG-TCTCG-AAAGACA
1 TAGGTAATACTGTCCATATGTTC-CGTAAA-ACA
* *
2366986 TAGGTAATTCTGTCTATATGTTCCGTAAAACA
1 TAGGTAATACTGTCCATATGTTCCGTAAAACA
2367018 TAGGTAA
1 TAGGTAA
2367025 ACCCTCAACT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
30 5 0.09
31 24 0.41
32 24 0.41
33 5 0.09
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (32 bp):
TAGGTAATACTGTCCATATGTTCCGTAAAACA
Found at i:2367432 original size:16 final size:16
Alignment explanation
Indices: 2367411--2367448 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2367401 CATGTCACCC
*
2367411 TCATATGATTTCATA-T
1 TCATATGATAT-ATATT
2367427 TCATATGATATATATT
1 TCATATGATATATATT
2367443 TCATAT
1 TCATAT
2367449 TTTTTTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (16 bp):
TCATATGATATATATT
Found at i:2367539 original size:2 final size:2
Alignment explanation
Indices: 2367532--2367575 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2367522 ACATATTTAT
2367532 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2367574 CA
1 CA
2367576 TATATATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2367580 original size:2 final size:2
Alignment explanation
Indices: 2367575--2367618 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2367565 ACACACACAC
2367575 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2367617 AT
1 AT
2367619 TTACACAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2370274 original size:20 final size:22
Alignment explanation
Indices: 2370245--2370388 Score: 84
Period size: 23 Copynumber: 6.6 Consensus size: 22
2370235 AAAACCCGAC
* *
2370245 GAGTGTATCGATGCAC-TGC-T
1 GAGTGCATCGATGCACATGCAG
*
2370265 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATGC-AG
*
2370288 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATGC-AG
* * * * *
2370311 GAGTGCATCGGTGTACCTTCAT
1 GAGTGCATCGATGCACATGCAG
* * *
2370333 G-GTGTATCGATGCATATTCAAAG
1 GAGTGCATCGATGCACATGC--AG
*
2370356 GA-TGCATCGATGCAC-TG-AT
1 GAGTGCATCGATGCACATGCAG
*
2370375 GAGTGTATCGATGC
1 GAGTGCATCGATGC
2370389 TTTATGCACA
Statistics
Matches: 99, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
19 3 0.03
20 25 0.25
21 15 0.15
22 3 0.03
23 53 0.54
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (22 bp):
GAGTGCATCGATGCACATGCAG
Found at i:2370295 original size:23 final size:23
Alignment explanation
Indices: 2370265--2370370 Score: 128
Period size: 23 Copynumber: 4.7 Consensus size: 23
2370255 ATGCACTGCT
2370265 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
2370288 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* * * *
2370311 GAGTGCATCGGTGTACCTTC-AT
1 GAGTGCATCGATGCACATTCAAG
* *
2370333 G-GTGTATCGATGCATATTCAAAG
1 GAGTGCATCGATGCACATTC-AAG
2370356 GA-TGCATCGATGCAC
1 GAGTGCATCGATGCAC
2370371 TGATGAGTGT
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
21 13 0.19
22 2 0.03
23 53 0.78
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:2373986 original size:22 final size:21
Alignment explanation
Indices: 2373944--2373983 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2373934 AAGACTATTT
2373944 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
2373965 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
2373984 ATAGAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:2375979 original size:64 final size:66
Alignment explanation
Indices: 2375832--2375986 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 66
2375822 ACACTAAGGA
* * * * *
2375832 TGCATCGATGCATAAAATACATTC-ATTGTTTTAAAAAAGCCTGGAGTGCATCGACGCATGGTTT
1 TGCATCGATGCATAAAATGCATTCGATTGTTTCAAAAAAGCCTGCAGTGAATCAACGCATGGTTT
2375896 G
66 G
* *
2375897 TGCATCGATGCATAAAATGCATTCGA-TGTTTCAATAAAATCCT-CAGTGAATCAATGCATGG-T
1 TGCATCGATGCATAAAATGCATTCGATTGTTTCAA-AAAAGCCTGCAGTGAATCAACGCATGGTT
2375959 TG
65 TG
*
2375961 TGCATCGGTGCATAAAATGCATTCGA
1 TGCATCGATGCATAAAATGCATTCGA
2375987 AATGGGGTGT
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 28 0.35
65 44 0.55
66 8 0.10
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (66 bp):
TGCATCGATGCATAAAATGCATTCGATTGTTTCAAAAAAGCCTGCAGTGAATCAACGCATGGTTT
G
Found at i:2378748 original size:31 final size:31
Alignment explanation
Indices: 2378722--2378793 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
2378712 GTGTAATGGT
*
2378722 GAAAACGTTAGACACCTAAAAATGTAACGAA
1 GAAAACATTAGACACCTAAAAATGTAACGAA
*
2378753 GAAAACATTAGACACCTAAAAATATAACGAA
1 GAAAACATTAGACACCTAAAAATGTAACGAA
*
2378784 TAAAACATTA
1 GAAAACATTA
2378794 TCACCTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.56, C:0.15, G:0.11, T:0.18
Consensus pattern (31 bp):
GAAAACATTAGACACCTAAAAATGTAACGAA
Found at i:2379662 original size:30 final size:30
Alignment explanation
Indices: 2379626--2379684 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2379616 CAGTGACCAT
* * *
2379626 CATAGGTCTCCAGGAGCACATGGCGACCTC
1 CATAGGTCTCCAAGAGCACACGACGACCTC
*
2379656 CATAGGTCTCTAAGAGCACACGACGACCT
1 CATAGGTCTCCAAGAGCACACGACGACCT
2379685 ATGGAGCACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.27, C:0.32, G:0.24, T:0.17
Consensus pattern (30 bp):
CATAGGTCTCCAAGAGCACACGACGACCTC
Found at i:2379725 original size:19 final size:19
Alignment explanation
Indices: 2379669--2379712 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
2379659 AGGTCTCTAA
*
2379669 GAGCACACGACGACCTATG
1 GAGCACACGGCGACCTATG
2379688 GAGCACACGGCGACCTATG
1 GAGCACACGGCGACCTATG
2379707 GAGCAC
1 GAGCAC
2379713 TTGGCGACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.32, G:0.30, T:0.09
Consensus pattern (19 bp):
GAGCACACGGCGACCTATG
Found at i:2380339 original size:14 final size:14
Alignment explanation
Indices: 2380320--2380350 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2380310 TAATATTTGT
2380320 CTAAAAGAGCCATA
1 CTAAAAGAGCCATA
2380334 CTAAAAGAGCCATA
1 CTAAAAGAGCCATA
2380348 CTA
1 CTA
2380351 GTGTTTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.16
Consensus pattern (14 bp):
CTAAAAGAGCCATA
Found at i:2385404 original size:69 final size:69
Alignment explanation
Indices: 2385321--2385458 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
2385311 ATGTTTCATA
2385321 AGTTTCATGAGTTTCATGCATTTCAGTTATAAAAATTTCATGAGTTTCAGTTGCATTCTGATATA
1 AGTTTCATGAGTTTCATGCATTTCAGTTATAAAAATTTCATGAGTTTCAGTTGCATTCTGATATA
2385386 TGGT
66 TGGT
2385390 AGTTTCATGAGTTTCATGCATTTCAGTTATAAAAATTTCATGAGTTTCAGTTGCATTCTGATATA
1 AGTTTCATGAGTTTCATGCATTTCAGTTATAAAAATTTCATGAGTTTCAGTTGCATTCTGATATA
2385455 TGGT
66 TGGT
2385459 TTCAGTGGTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (69 bp):
AGTTTCATGAGTTTCATGCATTTCAGTTATAAAAATTTCATGAGTTTCAGTTGCATTCTGATATA
TGGT
Found at i:2388320 original size:21 final size:21
Alignment explanation
Indices: 2388294--2388333 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2388284 CATATTGCTC
2388294 AGAGGGAACCGATTCCCCCCA
1 AGAGGGAACCGATTCCCCCCA
* *
2388315 AGAGGGTACTGATTCCCCC
1 AGAGGGAACCGATTCCCCC
2388334 TGAATGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.15
Consensus pattern (21 bp):
AGAGGGAACCGATTCCCCCCA
Found at i:2393998 original size:23 final size:23
Alignment explanation
Indices: 2393961--2394023 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2393951 TTGGTGCAGA
* *
2393961 GGGAATCGATACCCCCCTTGAAG
1 GGGAACCGATTCCCCCCTTGAAG
* *
2393984 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTGAAG
2394007 GGGAACCGATTCCCCCC
1 GGGAACCGATTCCCCCC
2394024 ATAGGGGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCTTGAAG
Found at i:2394031 original size:21 final size:22
Alignment explanation
Indices: 2393961--2394043 Score: 69
Period size: 23 Copynumber: 3.7 Consensus size: 22
2393951 TTGGTGCAGA
* * *
2393961 GGGAATCGATACCCCCCTTGAAG
1 GGGAACCGATTCCCCCCAT-AAG
* **
2393984 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCAT-AAG
2394007 GGGAACCGATTCCCCCCAT-AG
1 GGGAACCGATTCCCCCCATAAG
* *
2394028 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
2394044 TAGGGGTTCT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 16 0.31
23 35 0.69
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCATAAG
Found at i:2394047 original size:19 final size:21
Alignment explanation
Indices: 2394005--2394049 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2393995 CCCCCTTTGA
*
2394005 AGGGGAACCGATTCCCCCCAT
1 AGGGGAACCGATTACCCCCAT
*
2394026 AGGGGAATCGA-TACCCCC-T
1 AGGGGAACCGATTACCCCCAT
2394045 AGGGG
1 AGGGG
2394050 TTCTGGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 6 0.27
21 10 0.45
ACGTcount: A:0.24, C:0.31, G:0.31, T:0.13
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAT
Found at i:2400915 original size:15 final size:15
Alignment explanation
Indices: 2400895--2400924 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2400885 GGAATCTATG
2400895 ATAGTTGCATACGGT
1 ATAGTTGCATACGGT
2400910 ATAGTTGCATACGGT
1 ATAGTTGCATACGGT
2400925 TATTCTCCTA
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:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (15 bp):
ATAGTTGCATACGGT
Found at i:2411016 original size:31 final size:30
Alignment explanation
Indices: 2410981--2411043 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
2410971 TTTTTGAGTC
*
2410981 TATAAAGGAAAAAGTTAAAATTATATTTATA
1 TATAAAGAAAAAAG-TAAAATTATATTTATA
* *
2411012 TATAAATAAAAAAGTCAAATTATATTTATA
1 TATAAAGAAAAAAGTAAAATTATATTTATA
2411042 TA
1 TA
2411044 GCATCAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (30 bp):
TATAAAGAAAAAAGTAAAATTATATTTATA
Found at i:2412360 original size:10 final size:10
Alignment explanation
Indices: 2412324--2412362 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2412314 CATCTCATAA
2412324 ATATTATGAT
1 ATATTATGAT
* *
2412334 ATATTTTTAT
1 ATATTATGAT
2412344 GATATTATGAT
1 -ATATTATGAT
2412355 ATATTATG
1 ATATTATG
2412363 TTAAACAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (10 bp):
ATATTATGAT
Found at i:2414497 original size:14 final size:14
Alignment explanation
Indices: 2414469--2414501 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2414459 ATGCATAAAT
2414469 ACTAATAAAACTAA
1 ACTAATAAAACTAA
2414483 ACTAAGTAAAA-TAA
1 ACTAA-TAAAACTAA
2414497 ACTAA
1 ACTAA
2414502 AATAGTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.64, C:0.12, G:0.03, T:0.21
Consensus pattern (14 bp):
ACTAATAAAACTAA
Found at i:2414696 original size:3 final size:3
Alignment explanation
Indices: 2414688--2414716 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2414678 GAGACTATCA
2414688 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2414717 CAAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2415867 original size:22 final size:23
Alignment explanation
Indices: 2415842--2415890 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
2415832 TATTAGTGCT
2415842 TAAAATAAAATAAT-ATAATGA-A
1 TAAAA-AAAATAATAATAATGACA
*
2415864 TAAAAATAATAATAATAATGACA
1 TAAAAAAAATAATAATAATGACA
2415887 TAAA
1 TAAA
2415891 GTAATACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 12 0.50
23 5 0.21
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (23 bp):
TAAAAAAAATAATAATAATGACA
Found at i:2420303 original size:12 final size:12
Alignment explanation
Indices: 2420288--2420322 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
2420278 AAAAATGAAA
2420288 AAAAAAGAAAAG
1 AAAAAAGAAAAG
2420300 AAAAAAGAAAAG
1 AAAAAAGAAAAG
*
2420312 AGAAAAGAAAA
1 AAAAAAGAAAA
2420323 TAAGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:2423231 original size:57 final size:58
Alignment explanation
Indices: 2423160--2423281 Score: 192
Period size: 57 Copynumber: 2.1 Consensus size: 58
2423150 AGTCAATTTT
* * * *
2423160 AACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTTCAGTTT-ATTTAGAGTC
1 AACTTCACAACGAAGGATATTGGACTCAACAAAAAACTTTTCAATTTCATTCAGAGTC
2423217 AACTTCACAACGAAGGATATTGGACTCAACAAAAAACTTTTCAATTTCATTCAGAGTC
1 AACTTCACAACGAAGGATATTGGACTCAACAAAAAACTTTTCAATTTCATTCAGAGTC
*
2423275 AATTTCA
1 AACTTCA
2423282 ACTTCACATC
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
57 44 0.75
58 15 0.25
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.30
Consensus pattern (58 bp):
AACTTCACAACGAAGGATATTGGACTCAACAAAAAACTTTTCAATTTCATTCAGAGTC
Found at i:2423413 original size:48 final size:48
Alignment explanation
Indices: 2423263--2423413 Score: 124
Period size: 48 Copynumber: 3.0 Consensus size: 48
2423253 CTTTTCAATT
* *
2423263 TCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGAACTGAAAGAAA
1 TCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACT----CAAA
** * * ** * *
2423315 TACAACCAAAAATTGGATTTTAACTTCACAACGAAGGATATCT-AATTCAAA
1 T-CATTC--AGAGTCAATTTCAACTTCACAACGAAGGATAT-TGAACTCAAA
*
2423366 TCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAA
1 TCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAAA
2423414 GCAATACAAT
Statistics
Matches: 75, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
47 1 0.01
48 33 0.44
50 3 0.04
51 4 0.05
52 1 0.01
53 3 0.04
55 29 0.39
56 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (48 bp):
TCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAAA
Found at i:2423443 original size:103 final size:103
Alignment explanation
Indices: 2423263--2423468 Score: 340
Period size: 103 Copynumber: 2.0 Consensus size: 103
2423253 CTTTTCAATT
* *
2423263 TCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGAACTGAAAGAAATACAACCAAAAAT
1 TCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAAGAAATACAACCAAAAAT
* *
2423328 TGGATTTTAACTTCACAACGAAGGATATCTAATTCAAA
66 TGGATTTCAACTTCACAACGAAGGATATCCAATTCAAA
* * *
2423366 TCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAAGCAATACAATCAAAGAT
1 TCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAAGAAATACAACCAAAAAT
*
2423431 TGGATTTCAACTTCACGACGAAGGATATCCAATTCAAA
66 TGGATTTCAACTTCACAACGAAGGATATCCAATTCAAA
2423469 GCTCAACTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (103 bp):
TCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAAGAAATACAACCAAAAAT
TGGATTTCAACTTCACAACGAAGGATATCCAATTCAAA
Found at i:2423703 original size:151 final size:151
Alignment explanation
Indices: 2423429--2423781 Score: 562
Period size: 151 Copynumber: 2.3 Consensus size: 151
2423419 ACAATCAAAG
* * *
2423429 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCAAAATGAATGAGTCA
1 ATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAAAATGAAGGAGCCA
* *
2423494 TCCACGATTTCAACTCCACGATGGAGGATATCGTGCCCACACATCCACGATTTCAACTTCACAAT
66 TCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACACATCCACGATTTCAACTTCACAAC
2423559 GAAGGATATCGTGTCAACAAC
131 GAAGGATATCGTGTCAACAAC
* * *
2423580 ATTGGATTTCAACTTCACTATGAATGATATCCAATTCAAAGCTCAACTTCAAAATGAAGGAGCCA
1 ATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAAAATGAAGGAGCCA
* * *
2423645 TCTACGATTTCAACTCCACGACGGAGGATATTGTGCCCACACATCCACGATTTCAACTTCACGAC
66 TCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACACATCCACGATTTCAACTTCACAAC
* *
2423710 GAAGGATATTGTGTCAGCAAC
131 GAAGGATATCGTGTCAACAAC
* * *
2423731 ATTGAATTTCAACTTCACAACAAAGGATATCCAATTCAAAACTCAACTTCA
1 ATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCA
2423782 CAGCGAAAGG
Statistics
Matches: 184, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
151 184 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (151 bp):
ATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAAAATGAAGGAGCCA
TCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACACATCCACGATTTCAACTTCACAAC
GAAGGATATCGTGTCAACAAC
Found at i:2424270 original size:137 final size:137
Alignment explanation
Indices: 2424025--2424813 Score: 1090
Period size: 137 Copynumber: 5.8 Consensus size: 137
2424015 TCGTGTCCAT
2424025 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAA-CGTGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
*
2424089 AAAGATGGCCAGACGTCCTCATCATGAAGGAACAATGTCATCCACTGATCAGAACTCCTCATCAC
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAACTCCTCATCAC
*
2424154 AAAGGAG
131 GAAGGAG
* *
2424161 CAACACCATTCTTAGATAGCCAGATGTCCTCATCATGAAGGAACCGTGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
* * *
2424226 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCGTCATCAT
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAACTCCTCATCAC
2424291 GAAGGAG
131 GAAGGAG
* * * * *
2424298 CAACATCATCCTTAGATAGCCAAATTTCCTCATCATGAAGGAACCTTGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
* * * * *
2424363 AAAGATGGCTAGACGTCCTCATCACGAAGAAACAATGTCATCTACCGATCAGAACTCCTCATAAC
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAACTCCTCATCAC
*
2424428 GAAGGAA
131 GAAGGAG
*
2424435 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATATCAAATATCTTT
1 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
* * * *
2424500 AAAGATGACCAGATGTCCTCATCATGAAGGAACAATGTCATCCA-TCGATTAGAACTCCTCATCA
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACT-GATCAGAACTCCTCATCA
*
2424564 CGTAGGAG
130 CGAAGGAG
* * * * *
2424572 C--CGAGTCATTCTTAGATGGCTAGATGTCTTCATCACGAAGGAACCATGTTATCTCAAATGTCT
1 CAAC-A-TCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCT
*
2424635 TTAAAGATGGCTAGACGTCCTCATCACGAAGGAACAATGTCAT-CACTGA-CTAGAACTCCTCAT
64 TTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACTGATC-AGAACTCCTCAT
*
2424698 CACGTAGGAG
128 CACGAAGGAG
** * * * * *
2424708 C--CGAGTCAACCTCAGATAACCAGACGTTCTTATCACGAAGGAACCGTGTTATCTCAAATATCT
1 CAAC-A-TCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCT
* * * *
2424771 TCAAAGATGGCTAGACGTTCTCATCATGAAGGAACAATGTCAT
64 TTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCAT
2424814 ACACCAGTTG
Statistics
Matches: 585, Mismatches: 62, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
135 1 0.00
136 159 0.27
137 425 0.73
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (137 bp):
CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAACTCCTCATCAC
GAAGGAG
Found at i:2426084 original size:22 final size:22
Alignment explanation
Indices: 2426059--2426100 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2426049 TGCTTAAAAT
2426059 AAAATAAAATAAT-ATAATGAAG
1 AAAA-AAAATAATAATAATGAAG
*
2426081 AAAAATAATAATAATAATGA
1 AAAAAAAATAATAATAATGA
2426101 CATAAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (22 bp):
AAAAAAAATAATAATAATGAAG
Found at i:2434249 original size:2 final size:2
Alignment explanation
Indices: 2434242--2434297 Score: 94
Period size: 2 Copynumber: 27.5 Consensus size: 2
2434232 CCAAACATAA
2434242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2434284 AT TT AT AT CAT AT A
1 AT AT AT AT -AT AT A
2434298 CATACATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 49 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2434538 original size:23 final size:23
Alignment explanation
Indices: 2434508--2434560 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
2434498 AATGCAACGG
* *
2434508 AGTGCCACGTGGAATTACACCGA
1 AGTGCCACGTAGAAATACACCGA
* *
2434531 AGTGCCACGTAGAAATGCACCGT
1 AGTGCCACGTAGAAATACACCGA
2434554 AGTGCCA
1 AGTGCCA
2434561 TATAAGACGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
AGTGCCACGTAGAAATACACCGA
Found at i:2434842 original size:30 final size:29
Alignment explanation
Indices: 2434789--2434846 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
2434779 TGTAAACATA
* *
2434789 TCACATATTCATATAAACTCGTAGCTTCAG
1 TCACATATACATATAAACACGTAG-TTCAG
* *
2434819 TCACATATACATTTAATCACGTAGTTCA
1 TCACATATACATATAAACACGTAGTTCA
2434847 TGTAAATTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAG
Found at i:2439346 original size:23 final size:23
Alignment explanation
Indices: 2439312--2439380 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
2439302 CACCACAGAT
*
2439312 CGTATAAATGCACC-AGAGTGCCA
1 CGTAGAAATGCACCGA-AGTGCCA
* *
2439335 CGTAGAATTGCACCGAAGTGCTA
1 CGTAGAAATGCACCGAAGTGCCA
*
2439358 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2439381 TATAAGATGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2439661 original size:30 final size:29
Alignment explanation
Indices: 2439609--2439665 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
2439599 GTAAACATAA
* *
2439609 CACATATTCATATAAACTCGTAGCTTCAGT
1 CACATATACATATAAACACGTAG-TTCAGT
* *
2439639 CACATATACATTTAATCACGTAGTTCA
1 CACATATACATATAAACACGTAGTTCA
2439666 TGTAAATTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 4 0.17
30 19 0.83
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (29 bp):
CACATATACATATAAACACGTAGTTCAGT
Found at i:2446004 original size:22 final size:22
Alignment explanation
Indices: 2445966--2446007 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2445956 TCTTAGTATT
*
2445966 GGATTAAATGGTAATTATGGAA
1 GGATTAAATAGTAATTATGGAA
2445988 GGATTGAAATAGT-ATTATGG
1 GGATT-AAATAGTAATTATGG
2446008 TCTTTATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (22 bp):
GGATTAAATAGTAATTATGGAA
Found at i:2446209 original size:11 final size:11
Alignment explanation
Indices: 2446193--2446253 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
2446183 GGTGTTATAT
2446193 AAGCTTAAGGA
1 AAGCTTAAGGA
*
2446204 AAGCTTATA--T
1 AAGCTTA-AGGA
2446214 AAGCTTAAGGA
1 AAGCTTAAGGA
*
2446225 AAGCTTATA--T
1 AAGCTTA-AGGA
2446235 AAGCTTAAGGA
1 AAGCTTAAGGA
2446246 AAGCTTAA
1 AAGCTTAA
2446254 AACATCAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
9 2 0.05
10 14 0.35
11 22 0.55
12 2 0.05
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (11 bp):
AAGCTTAAGGA
Found at i:2446213 original size:21 final size:21
Alignment explanation
Indices: 2446187--2446252 Score: 132
Period size: 21 Copynumber: 3.1 Consensus size: 21
2446177 TTTTTGGGTG
2446187 TTATATAAGCTTAAGGAAAGC
1 TTATATAAGCTTAAGGAAAGC
2446208 TTATATAAGCTTAAGGAAAGC
1 TTATATAAGCTTAAGGAAAGC
2446229 TTATATAAGCTTAAGGAAAGC
1 TTATATAAGCTTAAGGAAAGC
2446250 TTA
1 TTA
2446253 AAACATCAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.30
Consensus pattern (21 bp):
TTATATAAGCTTAAGGAAAGC
Found at i:2460764 original size:21 final size:21
Alignment explanation
Indices: 2460738--2460795 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
2460728 ATTATCTAAT
*
2460738 AACTTGACATCCATAACAACA
1 AACTTGAAATCCATAACAACA
* *
2460759 AACTTGAAATCTATAACAAGA
1 AACTTGAAATCCATAACAACA
*
2460780 AACTTGAAACCCATAA
1 AACTTGAAATCCATAA
2460796 TAATAAATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.50, C:0.22, G:0.07, T:0.21
Consensus pattern (21 bp):
AACTTGAAATCCATAACAACA
Found at i:2462968 original size:29 final size:29
Alignment explanation
Indices: 2462932--2463043 Score: 197
Period size: 29 Copynumber: 3.8 Consensus size: 29
2462922 CAAACTAAAT
*
2462932 TGATGTCATTACTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
*
2462961 AGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
2462990 TGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
2463019 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
2463044 GTTAGGTGAG
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 74 0.94
30 5 0.06
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAATTAA
Found at i:2467766 original size:29 final size:29
Alignment explanation
Indices: 2467730--2467841 Score: 197
Period size: 29 Copynumber: 3.8 Consensus size: 29
2467720 CAAACTAAAT
*
2467730 TGATGTCATTACTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
*
2467759 AGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
2467788 TGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
2467817 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
2467842 GTTAGGTGAG
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 74 0.94
30 5 0.06
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAATTAA
Found at i:2468474 original size:41 final size:40
Alignment explanation
Indices: 2468429--2468559 Score: 131
Period size: 41 Copynumber: 3.2 Consensus size: 40
2468419 TATAAATGTT
* * *
2468429 ACTAAAATATGAGTATTTATCGATGTTTGTTCAAAAACATC
1 ACTAAAATATGAGTATTTAGCGGTGTTTATTCAAAAAC-TC
* * *
2468470 ACTAAAGTAT-AGAATTTAGCGGCGTTTATAT-AAAAACTCC
1 ACTAAAATATGAGTATTTAGCGGTGTTTAT-TCAAAAACT-C
* * *
2468510 ACTAAAATATGAGTCTTTAGCGGTGTTTATACAAAAACGCC
1 ACTAAAATATGAGTATTTAGCGGTGTTTATTCAAAAAC-TC
2468551 ACTAAAATA
1 ACTAAAATA
2468560 CAGTATTAAG
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
39 1 0.01
40 30 0.41
41 42 0.58
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (40 bp):
ACTAAAATATGAGTATTTAGCGGTGTTTATTCAAAAACTC
Found at i:2469485 original size:21 final size:21
Alignment explanation
Indices: 2469461--2469591 Score: 69
Period size: 21 Copynumber: 6.3 Consensus size: 21
2469451 AAATCGTAAT
* *
2469461 GCGATTTTCTAAATTCGCAAC
1 GCGATTATGTAAATTCGCAAC
*
2469482 GCGAATATGTAAA-TCGCAAC
1 GCGATTATGTAAATTCGCAAC
** * *
2469502 GATAATATGTAAA-TCGCAAT
1 GCGATTATGTAAATTCGCAAC
*
2469522 GC-AGTT-TTTCAAATTCGCAAC
1 GCGA-TTATGT-AAATTCGCAAC
*
2469543 GTC-ATT-TTTCAAATTCGCAAC
1 G-CGATTATGT-AAATTCGCAAC
* *
2469564 GTGAATATGTAAATT-GCAAC
1 GCGATTATGTAAATTCGCAAC
2469584 GCTGATTA
1 GC-GATTA
2469592 CTGATGTAGG
Statistics
Matches: 88, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
19 3 0.03
20 35 0.40
21 46 0.52
22 4 0.05
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (21 bp):
GCGATTATGTAAATTCGCAAC
Found at i:2469500 original size:20 final size:20
Alignment explanation
Indices: 2469470--2469520 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2469460 TGCGATTTTC
*
2469470 TAAATTCGCAACGCGAATATG
1 TAAA-TCGCAACGAGAATATG
*
2469491 TAAATCGCAACGATAATATG
1 TAAATCGCAACGAGAATATG
2469511 TAAATCGCAA
1 TAAATCGCAA
2469521 TGCAGTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.24
Consensus pattern (20 bp):
TAAATCGCAACGAGAATATG
Found at i:2469584 original size:20 final size:21
Alignment explanation
Indices: 2469470--2469584 Score: 82
Period size: 21 Copynumber: 5.6 Consensus size: 21
2469460 TGCGATTTTC
*
2469470 TAAATTCGCAACGCGAATATG
1 TAAATTCGCAACGTGAATATG
2469491 TAAA-TCGCAACGAT-AATATG
1 TAAATTCGCAACG-TGAATATG
* * *
2469511 TAAA-TCGCAA--TGCAGTTTT
1 TAAATTCGCAACGTG-AATATG
* * *
2469530 TCAAATTCGCAACGT-CATTTT
1 T-AAATTCGCAACGTGAATATG
2469551 TCAAATTCGCAACGTGAATATG
1 T-AAATTCGCAACGTGAATATG
2469573 TAAATT-GCAACG
1 TAAATTCGCAACG
2469585 CTGATTACTG
Statistics
Matches: 77, Mismatches: 9, Indels: 17
0.75 0.09 0.17
Matches are distributed among these distances:
17 1 0.01
19 4 0.05
20 33 0.43
21 34 0.44
22 4 0.05
23 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (21 bp):
TAAATTCGCAACGTGAATATG
Found at i:2469646 original size:20 final size:20
Alignment explanation
Indices: 2469618--2469661 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2469608 GTACTATCGT
*
2469618 AACGCGATTTTCAAATTCGC
1 AACGAGATTTTCAAATTCGC
2469638 AACGAGATTTTCAAATTCGC
1 AACGAGATTTTCAAATTCGC
2469658 AACG
1 AACG
2469662 CTAATTGCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (20 bp):
AACGAGATTTTCAAATTCGC
Found at i:2469679 original size:77 final size:77
Alignment explanation
Indices: 2469548--2469716 Score: 234
Period size: 77 Copynumber: 2.2 Consensus size: 77
2469538 GCAACGTCAT
* * * *
2469548 TTTTCAAATTCGCAACGTGAATATGTAAATTGCAACGCTGATTACTGATGTAGGTAAACAGTACT
1 TTTTCAAATTCGCAACGAGAATATGTAAATTGCAACGCTAATTACCGATATAGGTAAACAGTACT
*
2469613 ATCGTAACGCGA
66 ATCGCAACGCGA
* *
2469625 TTTTCAAATTCGCAACGAG-AT-TTTCAAATTCGCAACGCTAATTGCCGATATAGGTAAACAGTA
1 TTTTCAAATTCGCAACGAGAATATGT-AAATT-GCAACGCTAATTACCGATATAGGTAAACAGTA
2469688 CTATCGCAACGCGA
64 CTATCGCAACGCGA
*
2469702 TTTACAAATTCGCAA
1 TTTTCAAATTCGCAA
2469717 ATAAAAATCG
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
75 2 0.02
76 7 0.09
77 73 0.89
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (77 bp):
TTTTCAAATTCGCAACGAGAATATGTAAATTGCAACGCTAATTACCGATATAGGTAAACAGTACT
ATCGCAACGCGA
Found at i:2469953 original size:40 final size:40
Alignment explanation
Indices: 2469897--2469982 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
2469887 ATTAAAATCG
* *
2469897 TATATTATAAGGCATTTTCGGTTACTGAAGTTACTTTCTC
1 TATATTATAAGACATTTTCGGTCACTGAAGTTACTTTCTC
*
2469937 TATATTATAAGACATTTTCGGTCACTGAAGTTATTTTCTC
1 TATATTATAAGACATTTTCGGTCACTGAAGTTACTTTCTC
*
2469977 TTTATT
1 TATATT
2469983 TTATGGATAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.48
Consensus pattern (40 bp):
TATATTATAAGACATTTTCGGTCACTGAAGTTACTTTCTC
Found at i:2471288 original size:20 final size:20
Alignment explanation
Indices: 2471263--2471302 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2471253 AATCAGATTG
2471263 TCCAGGGGGTACAGATTCCC
1 TCCAGGGGGTACAGATTCCC
*
2471283 TCCAGGGGGTACCGATTCCC
1 TCCAGGGGGTACAGATTCCC
2471303 CCCACGCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.33, G:0.30, T:0.20
Consensus pattern (20 bp):
TCCAGGGGGTACAGATTCCC
Found at i:2475588 original size:3 final size:3
Alignment explanation
Indices: 2475575--2475621 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
2475565 AGTCCTTTAT
* * *
2475575 TTA TAA TTA TTA TTA TT- TTA TTA TTT TTA CCTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
2475620 TT
1 TT
2475622 TTCCTTTCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2475712 original size:23 final size:22
Alignment explanation
Indices: 2475668--2475726 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
2475658 ATAGTATTTA
*
2475668 TTTTATTTATTATTTTTTTCTC
1 TTTTATTTATTTTTTTTTTCTC
*
2475690 TTTTCTTTATTTTTGTTTTTCTC
1 TTTTATTTATTTTT-TTTTTCTC
*
2475713 -ATTATTTATTTTTT
1 TTTTATTTATTTTTT
2475727 ATATCTAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 1 0.03
22 23 0.72
23 8 0.25
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTATTTATTTTTTTTTTCTC
Found at i:2476653 original size:20 final size:20
Alignment explanation
Indices: 2476630--2476675 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2476620 ATATATATAC
*
2476630 ATTTTTTATA-TTTTATTATT
1 ATTTTTTATAGTTTT-TAATT
*
2476650 ATTTTATATAGTTTTTAATT
1 ATTTTTTATAGTTTTTAATT
2476670 ATTTTT
1 ATTTTT
2476676 GGTTATTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
ATTTTTTATAGTTTTTAATT
Found at i:2477099 original size:13 final size:13
Alignment explanation
Indices: 2477083--2477125 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
2477073 TATTCTTTTA
2477083 TTTTCTTTTCTAT
1 TTTTCTTTTCTAT
2477096 TTTTCTTTATCCTTAT
1 TTTTCTTT-T-C-TAT
*
2477112 TTTTCTTTTGTAT
1 TTTTCTTTTCTAT
2477125 T
1 T
2477126 CGGATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 12 0.46
14 1 0.04
15 2 0.08
16 11 0.42
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTTCTTTTCTAT
Found at i:2477101 original size:23 final size:22
Alignment explanation
Indices: 2477045--2477103 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
2477035 ATATTTACTA
2477045 TTATC-TTTCTTTTTATATTTTT
1 TTATCTTTTC-TTTTATATTTTT
*
2477067 TTATCTTATTCTTTTATTTTCTTT
1 TTATCTT-TTCTTTTATATT-TTT
2477091 TCTAT-TTTTCTTT
1 T-TATCTTTTCTTT
2477104 ATCCTTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 5 0.16
23 15 0.47
24 9 0.28
25 3 0.09
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATCTTTTCTTTTATATTTTT
Found at i:2487983 original size:14 final size:14
Alignment explanation
Indices: 2487964--2487990 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2487954 GATCGAAACT
2487964 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
2487978 TCAAGATTCCAGA
1 TCAAGATTCCAGA
2487991 CAGGCAACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:2488474 original size:106 final size:105
Alignment explanation
Indices: 2488347--2488881 Score: 741
Period size: 106 Copynumber: 5.0 Consensus size: 105
2488337 ATATCGCACC
* ** * * * *
2488347 ACTCGAGACAACACAAGTTCAACTTCACAACGAAATGACGACTGGTTGTCAATGAAAATTTTCCT
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-AAAAAATTTCCC
2488412 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
2488453 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTATCAATAAAAAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-AAAAAATTTCCC
* * *
2488518 AATCTCAGAGCCAATTTCAACTTCACATCGAATGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
2488559 ACT-ATAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAAAATTTCC
1 ACTCA-AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-AAAAAATTTCC
* *
2488623 CAATCTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2488665 ACTCGAGATAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-AAAAAATTTCCC
* * **
2488730 AGTTTCAGAGCCAATTTCAACTTTACAATGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2488771 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-AAAAAATTTCCC
* * *
2488836 AGTTCCAGAGCCAATTTCAACTTCACGGCGGAA-GATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGC-GAAGGATATTGG
2488877 ACTCA
1 ACTCA
2488882 TAACAGTACA
Statistics
Matches: 392, Mismatches: 34, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
105 1 0.00
106 388 0.99
107 3 0.01
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (105 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAAAAAAATTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:2490242 original size:20 final size:20
Alignment explanation
Indices: 2490219--2490263 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2490209 TATATATACG
*
2490219 TTTTTTATA-TTTTATTATTA
1 TTTTTTATAGTTTT-TAATTA
*
2490239 TTTTATATAGTTTTTAATTA
1 TTTTTTATAGTTTTTAATTA
2490259 TTTTT
1 TTTTT
2490264 GGTTATTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTTATAGTTTTTAATTA
Found at i:2490657 original size:23 final size:23
Alignment explanation
Indices: 2490628--2490687 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
2490618 ATATTTACTA
2490628 TTATCTTTCTTTTTATATTT-TTT
1 TTATCTTTCTTTTTAT-TTTCTTT
2490651 TTATCTTAT-TCTTTTATTTTCTTT
1 TTATCTT-TCT-TTTTATTTTCTTT
*
2490675 TCTATTTTTCTTT
1 T-TATCTTTCTTT
2490688 ATCCTTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
23 11 0.35
24 14 0.45
25 6 0.19
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (23 bp):
TTATCTTTCTTTTTATTTTCTTT
Found at i:2490673 original size:35 final size:37
Alignment explanation
Indices: 2490628--2490696 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 37
2490618 ATATTTACTA
*
2490628 TTATCTTTCTTTT-TATATTTTTTTTAT-CTTATTCTT
1 TTATCTTTCTTTTCTAT-TTTTCTTTATCCTTATTCTT
2490664 TTAT-TTTCTTTTCTATTTTTCTTTATCCTTATT
1 TTATCTTTCTTTTCTATTTTTCTTTATCCTTATT
2490697 TTTCTTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (37 bp):
TTATCTTTCTTTTCTATTTTTCTTTATCCTTATTCTT
Found at i:2490683 original size:13 final size:13
Alignment explanation
Indices: 2490667--2490709 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
2490657 TATTCTTTTA
2490667 TTTTCTTTTCTAT
1 TTTTCTTTTCTAT
2490680 TTTTCTTTATCCTTAT
1 TTTTCTTT-T-C-TAT
*
2490696 TTTTCTTTTGTAT
1 TTTTCTTTTCTAT
2490709 T
1 T
2490710 CGGATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 12 0.46
14 1 0.04
15 2 0.08
16 11 0.42
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTTCTTTTCTAT
Found at i:2490686 original size:29 final size:30
Alignment explanation
Indices: 2490649--2490709 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
2490639 TTTATATTTT
* *
2490649 TTTTATC-TTATTCTTTTATTTTCTTTTCTA
1 TTTTATCTTTATCCTTAT-TTTTCTTTTCTA
*
2490679 TTTT-TCTTTATCCTTATTTTTCTTTTGTA
1 TTTTATCTTTATCCTTATTTTTCTTTTCTA
2490708 TT
1 TT
2490710 CGGATAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.74
Consensus pattern (30 bp):
TTTTATCTTTATCCTTATTTTTCTTTTCTA
Found at i:2496520 original size:22 final size:22
Alignment explanation
Indices: 2496470--2496520 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
2496460 AGATTCAATC
*
2496470 AAGAACAAAAAAGAAAAGAAGCAA
1 AAGAA-AAAAAAAAAAAGAAG-AA
*
2496494 AA-AAAAAAATAAAAAGAA-AA
1 AAGAAAAAAAAAAAAAGAAGAA
2496514 AAGAAAA
1 AAGAAAA
2496521 GAAGCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 12 0.50
23 2 0.08
24 2 0.08
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (22 bp):
AAGAAAAAAAAAAAAAGAAGAA
Found at i:2496554 original size:28 final size:28
Alignment explanation
Indices: 2496477--2496541 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
2496467 ATCAAGAACA
2496477 AAAAAGAAAAGAAGCAAAA-AA--AAAAAT
1 AAAAAGAAAA-AAG-AAAAGAAGCAAAAAT
2496504 AAAAAGAAAAAAGAAAAGAAGCAAAAAT
1 AAAAAGAAAAAAGAAAAGAAGCAAAAAT
*
2496532 CAAAAGAAAA
1 AAAAAGAAAA
2496542 GGGACAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 4 0.12
26 5 0.15
27 10 0.29
28 15 0.44
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (28 bp):
AAAAAGAAAAAAGAAAAGAAGCAAAAAT
Found at i:2497612 original size:18 final size:18
Alignment explanation
Indices: 2497589--2497624 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2497579 TCAACATCAA
*
2497589 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
2497607 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
2497625 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:2498150 original size:36 final size:37
Alignment explanation
Indices: 2498103--2498174 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 37
2498093 GTGCTCACCA
*
2498103 TTGTCTCTCTTGAGACAGTTTCCCTT-GAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGGAAAAAAACT
2498139 TTGTCTCTCTTGAGACAGTTTCCCTTGGAAAAAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGGAAAAAAAC
2498175 CCTTGAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 26 0.76
37 8 0.24
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGGAAAAAAACT
Found at i:2499559 original size:106 final size:106
Alignment explanation
Indices: 2499041--2499565 Score: 806
Period size: 106 Copynumber: 5.0 Consensus size: 106
2499031 TCGCGCCACC
* *
2499041 CGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
*
2499106 TTCAGAGCCAATTTCAACTTCACAGC--TGGATATTGGACT
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
* *
2499145 CAAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAA-AATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* **
2499209 TTCAGAGCCAATTTTAACTTCACAGCGAAGGGCATTGGACT
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
* **
2499250 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGATTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
** *
2499315 TTCAGAGCCAATTTCAACTTCACAATGAAGGACATTGGACT
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
*
2499356 CGAGACAGCACAAG-TCTAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAA
1 CGAGACAACACAAGTTC-AACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAA
* * *
2499420 TTTCAGAACCAATGTCAACTTCACAACGAAGGATATTGGACT
65 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
*
2499462 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* * * *
2499527 TCCAGAACCAATTTCAACTTCACGGCGGAGGATATTGGA
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
2499566 TTCAAAACAA
Statistics
Matches: 386, Mismatches: 30, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
103 35 0.09
104 50 0.13
105 62 0.16
106 237 0.61
107 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (106 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
Found at i:2501010 original size:16 final size:15
Alignment explanation
Indices: 2500975--2501022 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
2500965 TGTATCATTA
*
2500975 TTATTTTATTATTTAT
1 TTATTTTATT-TATAT
2500991 TTATTTTATTTATAT
1 TTATTTTATTTATAT
* *
2501006 GTTATATTATATATAT
1 -TTATTTTATTTATAT
2501022 T
1 T
2501023 ACGTTATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTATTTTATTTATAT
Found at i:2501695 original size:2 final size:2
Alignment explanation
Indices: 2501688--2501739 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
2501678 AACACCTATT
2501688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2501730 TA T- TA TA TA T
1 TA TA TA TA TA T
2501740 TTTTATTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2501981 original size:33 final size:33
Alignment explanation
Indices: 2501944--2502007 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
2501934 TCATTTTGTC
2501944 TTATTTTTATTTTATTTACTT-TATTATTTTCCT
1 TTATTTTT-TTTTATTTACTTGTATTATTTTCCT
**
2501977 TTATTTTTTTTTATTTTTTTGTATTATTTTC
1 TTATTTTTTTTTATTTACTTGTATTATTTTC
2502008 ATATTTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.77
Consensus pattern (33 bp):
TTATTTTTTTTTATTTACTTGTATTATTTTCCT
Found at i:2501994 original size:10 final size:10
Alignment explanation
Indices: 2501893--2502006 Score: 61
Period size: 10 Copynumber: 10.9 Consensus size: 10
2501883 ATTTCTTCCA
2501893 TTATTTTATTT
1 TTATTTT-TTT
2501904 TT-TTTTTTGT
1 TTATTTTTT-T
*
2501914 TTAGTTTTGTT
1 TTA-TTTTTTT
**
2501925 TTA-TTAATT
1 TTATTTTTTT
* * *
2501934 TCATTTTGTC
1 TTATTTTTTT
2501944 TTATTTTTATT
1 TTATTTTT-TT
*
2501955 TTATTTACTTTA
1 TTATTT--TTTT
**
2501967 TTATTTTCCT
1 TTATTTTTTT
2501977 TTATTTTTTT
1 TTATTTTTTT
2501987 TTATTTTTTT
1 TTATTTTTTT
*
2501997 GTATTATTTT
1 TTATT-TTTT
2502007 CATATTTTTG
Statistics
Matches: 78, Mismatches: 17, Indels: 16
0.70 0.15 0.14
Matches are distributed among these distances:
9 8 0.10
10 39 0.50
11 17 0.22
12 12 0.15
13 2 0.03
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:2504845 original size:200 final size:200
Alignment explanation
Indices: 2504490--2505825 Score: 1714
Period size: 200 Copynumber: 6.8 Consensus size: 200
2504480 TATTTAAATT
* *
2504490 AGTATCGACA-AAAATTAAAAAGTGTCGATACATGTTGTAG-CATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGTA
* *
2504553 TATTTATATCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
66 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
* * *
2504618 GATCGATACATTTTATAAATAGATCGACACTTTATGGTTGCACCCTTTTTGGGATTCATTCTGGA
131 GATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGA
2504683 CCAAA
196 CCAAA
* * *
2504688 AGTATCGAGACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTATCTCGTAAAACTGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGTA
*
2504753 TATTTATAGCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
66 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
*
2504818 GATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCATCCTTTTTGGCATTCATTCTGGA
131 GATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGA
*
2504883 GCAAA
196 CCAAA
2504888 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAA-CGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGTA
* * * *
2504952 AATCTATACCGGTTACATTGAAAAAGTACATATTACATTATACTTATGGGTTTCGATGTTTCTGG
66 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
** ** *
2505017 GATCGATAAATTTTATAAATATATCGACACTTTATGGTTGCACCCTTTTTTGCATTCATTCTGGA
131 GATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGA
2505082 CCAAA
196 CCAAA
*
2505087 AGTATCGACACAAAATTAAAAAG-GTTCGATACATGTTGTAGACCTATTCTCTCGTAAAATCGGT
1 AGTATCGACACAAAATTAAAAAGTG-TCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGT
* * *
2505151 ATATTTATATCAGTTACATTGAAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
65 ATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* * * ** * * ** * *
2505216 GGATCGATAC---TT-T--ATGG-TTGCACCCTTT-T--TGGCATTCATTCTGGACCA-AAAGTA
130 GGATCGATACTTTTTATAAATGGATCG-ACACTTTATGGTTGCACCCTTTTTGG--CATTCATTC
** *
2505270 TTAATACAAA
192 TGGA-CCAAA
* * * * * * * ** * *** *
2505280 A-T-T--A-A-AAACTGTTGATACA-TGTTGTATACCTATTCT-CTCGTAAAATC-GGT-AAA--
1 AGTATCGACACAAA--ATT-AAAAAGTGTCG-ATACATGTTGTAGACCTATTCTCTCGTAAAACC
* * * * * *
2505333 --T-T-TATA-CCGGTT-ACATTGAAAAATTACCTATTGCATTATACTTATGCGTTTCGATGTTT
62 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTT
** *
2505392 CTGGGATCGATACTTTTTATAAATATATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTT
127 CTGGGATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTC
2505457 TGGACCAAA
192 TGGACCAAA
*
2505466 AGTATCGACACAAAATTAAAAA-TGTTTGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGT
1 AGTATCGACACAAAATTAAAAAGTG-TCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGT
* *
2505530 ATATTTATAGCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
65 ATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
2505595 GGATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGG
130 GGATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGG
2505660 ACCAAA
195 ACCAAA
*
2505666 AGTATCGAAACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGTA
* *
2505731 AATTTATACAGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
66 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
*
2505796 GATCGATACTTTTTATATATGGATCGACAC
131 GATCGATACTTTTTATAAATGGATCGACAC
2505826 ATATGCTTAC
Statistics
Matches: 973, Mismatches: 122, Indels: 84
0.83 0.10 0.07
Matches are distributed among these distances:
179 57 0.06
180 1 0.00
181 3 0.00
182 3 0.00
183 2 0.00
185 8 0.01
186 10 0.01
187 11 0.01
188 14 0.01
189 23 0.02
190 23 0.02
191 13 0.01
192 11 0.01
193 10 0.01
194 8 0.01
196 2 0.00
197 3 0.00
198 13 0.01
199 216 0.22
200 540 0.55
201 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (200 bp):
AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGTA
TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
GATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGA
CCAAA
Found at i:2505348 original size:179 final size:179
Alignment explanation
Indices: 2505039--2505407 Score: 605
Period size: 179 Copynumber: 2.1 Consensus size: 179
2505029 TTATAAATAT
* * *
2505039 ATCGACACTTTATGGTTGCACCCTTTTTTGCATTCATTCTGGACCAAAAGTATCGACACAAAATT
1 ATCGATACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCAACACAAAATT
* *
2505104 AAAAAGGTTCGATACATGTTGTAGACCTATTCTCTCGTAAAATCGGTATATTTATATCAGTTACA
66 AAAAAGGTTCGATACATGTTGTAGACCTATTCTCTCGTAAAATCGGTAAATTTATACCAGTTACA
* *
2505169 TTGAAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGGG
131 TTGAAAAATTACCTATTACATTATACTTATGCGTTTCGATGTTTCTGGG
* *
2505218 ATCGATACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATTAATACAAAATT
1 ATCGATACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCAACACAAAATT
* * *
2505283 AAAAACTGTT-GATACATGTTGTATACCTATTCTCTCGTAAAATCGGTAAATTTATACCGGTTAC
66 AAAAA-GGTTCGATACATGTTGTAGACCTATTCTCTCGTAAAATCGGTAAATTTATACCAGTTAC
*
2505347 ATTGAAAAATTACCTATTGCATTATACTTATGCGTTTCGATGTTTCTGGG
130 ATTGAAAAATTACCTATTACATTATACTTATGCGTTTCGATGTTTCTGGG
2505397 ATCGATACTTT
1 ATCGATACTTT
2505408 TTATAAATAT
Statistics
Matches: 176, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
179 173 0.98
180 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (179 bp):
ATCGATACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGACCAAAAGTATCAACACAAAATT
AAAAAGGTTCGATACATGTTGTAGACCTATTCTCTCGTAAAATCGGTAAATTTATACCAGTTACA
TTGAAAAATTACCTATTACATTATACTTATGCGTTTCGATGTTTCTGGG
Found at i:2506090 original size:19 final size:19
Alignment explanation
Indices: 2506066--2506114 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2506056 TTACATTCAC
2506066 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
2506085 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
*
2506104 ATACAACATTA
1 ATACAAAATTA
2506115 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:2507935 original size:33 final size:33
Alignment explanation
Indices: 2507898--2507963 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2507888 CATCTTAAGA
* * *
2507898 TCACCCTTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTATTTCACCACT
*
2507931 TCACCCCTCAACACCTCTACTTATTTCACCACT
1 TCACCCCTCAACACCTCAACTTATTTCACCACT
2507964 CCATCAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTATTTCACCACT
Found at i:2508021 original size:21 final size:21
Alignment explanation
Indices: 2507997--2508040 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2507987 CCCCTTATGC
*
2507997 CTCTTAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
2508018 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
2508039 CT
1 CT
2508041 TGAATATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.30, G:0.11, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:2508143 original size:15 final size:15
Alignment explanation
Indices: 2508123--2508155 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2508113 ACTATGTTTT
*
2508123 CCCTCACCGTCATCC
1 CCCTCACCATCATCC
2508138 CCCTCACCATCATCC
1 CCCTCACCATCATCC
2508153 CCC
1 CCC
2508156 AATACAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.64, G:0.03, T:0.18
Consensus pattern (15 bp):
CCCTCACCATCATCC
Found at i:2510215 original size:28 final size:32
Alignment explanation
Indices: 2510183--2510244 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
2510173 CTTTCGAAAG
2510183 GATAA-TTA-CATATTT-CTT-TGAAAGTATC
1 GATAATTTATCATATTTACTTATGAAAGTATC
* *
2510211 GATAATTTATTATATTTACTTATTAAAGTATC
1 GATAATTTATCATATTTACTTATGAAAGTATC
2510243 GA
1 GA
2510245 CACTTTCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.18
29 3 0.11
30 6 0.21
31 3 0.11
32 11 0.39
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (32 bp):
GATAATTTATCATATTTACTTATGAAAGTATC
Found at i:2510602 original size:182 final size:182
Alignment explanation
Indices: 2510275--2510686 Score: 539
Period size: 182 Copynumber: 2.3 Consensus size: 182
2510265 GCACTTTACT
* *
2510275 GGTTTTATCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACAC
1 GGTTTTATCATATTTTTACATGTTATATCGTTGTGGATCAATACATTTTTACAAAGTATCGACAC
* * *
2510340 TTTATAGGCGCTAAAAGTGCTTCTCTTTTAAATTCACAAAGTGTCTATACTTATATTAAAGTACC
66 TTTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTACC
*
2510405 GACACTTTAAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTTGATATC
131 GACACGTTAAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTTGATATC
* * *
2510457 GGTTTTGTCATATTTTTACATGTTATATCTTTGTGGATTAATACATTTTTACAAAGTATCGACAC
1 GGTTTTATCATATTTTTACATGTTATATCGTTGTGGATCAATACATTTTTACAAAGTATCGACAC
* * * * *
2510522 TTTATAGGTGTTAAAACTATTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTATC
66 TTTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTACC
* * * * * *
2510587 GACACGTTCAATATATCCGGTAGTGTTTTATC-G--ATAGTC-TTTTCG-TGACC
131 GACACGTTAAATATATCCGGTAGCGCTTTACCGGTTTTA-TCATTTT-GAT-ATC
* * * *
2510637 GGTTTTATCATATTTTTACCTGTTATATTGATATGGAT-AATACATTTTTA
1 GGTTTTATCATATTTTTACATGTTATATCGTTGTGGATCAATACATTTTTA
2510687 ATTTGGATCG
Statistics
Matches: 201, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
179 19 0.09
180 37 0.18
181 1 0.00
182 144 0.72
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (182 bp):
GGTTTTATCATATTTTTACATGTTATATCGTTGTGGATCAATACATTTTTACAAAGTATCGACAC
TTTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTACC
GACACGTTAAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTTGATATC
Found at i:2510859 original size:11 final size:11
Alignment explanation
Indices: 2510843--2510883 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
2510833 AATAATACTG
*
2510843 TATATTAATTA
1 TATATTAACTA
*
2510854 TATATTAACTG
1 TATATTAACTA
2510865 TATATTAACTA
1 TATATTAACTA
2510876 TATATTAA
1 TATATTAA
2510884 TATGTCTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (11 bp):
TATATTAACTA
Done.