Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 51
Found at i:4295443 original size:20 final size:20
Alignment explanation
Indices: 4295418--4295462 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4295408 AAGGTACACT
*
4295418 TTCGCAACGTGAAAGCCAAA
1 TTCGCAACGCGAAAGCCAAA
* *
4295438 TTCGCAACGCGAAAGTCAAC
1 TTCGCAACGCGAAAGCCAAA
4295458 TTCGC
1 TTCGC
4295463 GTTTTGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (20 bp):
TTCGCAACGCGAAAGCCAAA
Found at i:4295715 original size:18 final size:18
Alignment explanation
Indices: 4295689--4295729 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
4295679 AGGTGAAGCC
*
4295689 GATTGTGATTGAGATTTT
1 GATTTTGATTGAGATTTT
*
4295707 GATTTTGATTGCGATTTT
1 GATTTTGATTGAGATTTT
4295725 GATTT
1 GATTT
4295730 CCTTTTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.54
Consensus pattern (18 bp):
GATTTTGATTGAGATTTT
Found at i:4298004 original size:24 final size:24
Alignment explanation
Indices: 4297977--4298030 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4297967 TTGAAACATC
4297977 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
4298001 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
4298025 ATCAAA
1 ATCAAA
4298031 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:4298804 original size:14 final size:15
Alignment explanation
Indices: 4298768--4298805 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
4298758 GAAATTATTG
4298768 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
4298783 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
4298798 AAAAATTA
1 AAAAATTA
4298806 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:4298842 original size:22 final size:21
Alignment explanation
Indices: 4298813--4298869 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 21
4298803 TTAGAGATGG
4298813 GGAAGGATGTCGTTGGATATA
1 GGAAGGATGTCGTTGGATATA
4298834 GGAACGGATGTCGTTGGATATA
1 GGAA-GGATGTCGTTGGATATA
*
4298856 TGAATGGATGTCGT
1 GGAA-GGATGTCGT
4298870 CAGAAAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.26, C:0.07, G:0.37, T:0.30
Consensus pattern (21 bp):
GGAAGGATGTCGTTGGATATA
Found at i:4299008 original size:20 final size:20
Alignment explanation
Indices: 4298967--4299021 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 20
4298957 AATATTTGTG
4298967 TTGCGAAATTAAAA--CCTA
1 TTGCGAAATTAAAATTCCTA
*
4298985 TTGCGAAATTAAAATTCGTA
1 TTGCGAAATTAAAATTCCTA
*
4299005 TTGCGAATTTGAAAATT
1 TTGCGAAATT-AAAATT
4299022 GAGTTGCTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 14 0.44
20 12 0.38
21 6 0.19
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (20 bp):
TTGCGAAATTAAAATTCCTA
Found at i:4299028 original size:20 final size:20
Alignment explanation
Indices: 4299005--4299128 Score: 54
Period size: 20 Copynumber: 6.2 Consensus size: 20
4298995 AAAATTCGTA
4299005 TTGCGAATTTGAAAATTGAG
1 TTGCGAATTTGAAAATTGAG
* *** *
4299025 TTGC-TATAACAAAATTCACG
1 TTGCGAATTTGAAAATTGA-G
* ** *
4299045 TCGCGAATTCAAAAATCGAG
1 TTGCGAATTTGAAAATTGAG
* ** *
4299065 TTACGAATTCAAAAATCGAG
1 TTGCGAATTTGAAAATTGAG
* *
4299085 TTGCGAAGTTG-AAATTTAG
1 TTGCGAATTTGAAAATTGAG
* *
4299104 TATTGCGAATTTGGAAACTGAG
1 --TTGCGAATTTGAAAATTGAG
4299126 TTG
1 TTG
4299129 TGAAATTGGA
Statistics
Matches: 76, Mismatches: 23, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
19 15 0.20
20 37 0.49
21 18 0.24
22 6 0.08
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
TTGCGAATTTGAAAATTGAG
Found at i:4304216 original size:3 final size:3
Alignment explanation
Indices: 4304208--4304233 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4304198 AGGGCAAAAC
4304208 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
4304234 ACAGACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4305193 original size:42 final size:42
Alignment explanation
Indices: 4305146--4305335 Score: 231
Period size: 42 Copynumber: 4.6 Consensus size: 42
4305136 CACAAACGTT
*
4305146 GCAATAGTCATGCACCTTAGCGGCGTTTTTATAATAAACGCC
1 GCAATAGTCATGCACCTTAGCGGCGTTTTTGTAATAAACGCC
* * * * *
4305188 GCAATAGCCATGCTCCTTAGTGGCGTTTTTGTAATAAACTCT
1 GCAATAGTCATGCACCTTAGCGGCGTTTTTGTAATAAACGCC
* * * **
4305230 GTAATAGTCATGCACCTTAGTGGAGTTTTTG--ATAAACATC
1 GCAATAGTCATGCACCTTAGCGGCGTTTTTGTAATAAACGCC
* *
4305270 GCAATAGTCATGCACCTTATCGGCGTTTTTGTAATAAACGTC
1 GCAATAGTCATGCACCTTAGCGGCGTTTTTGTAATAAACGCC
* *
4305312 ACAATTGTCATGCACCTTAGCGGC
1 GCAATAGTCATGCACCTTAGCGGC
4305336 AACAGTCATG
Statistics
Matches: 125, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
40 33 0.26
42 92 0.74
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (42 bp):
GCAATAGTCATGCACCTTAGCGGCGTTTTTGTAATAAACGCC
Found at i:4305288 original size:82 final size:84
Alignment explanation
Indices: 4305147--4305334 Score: 240
Period size: 82 Copynumber: 2.3 Consensus size: 84
4305137 ACAAACGTTG
* * *
4305147 CAATAGTCATGCACCTTAGCGGCGTTTTTATAATAAACGCCGCAATAGCCATGCTCCTTAGT-GG
1 CAATAGTCATGCACCTTAGCGGAGTTTTTATAATAAACACCGCAATAGCCATGCACCTTA-TCGG
*
4305211 CGTTTTTGTAATAAAC-TCTG
65 CGTTTTTGTAATAAACGTC-A
* * * * *
4305231 TAATAGTCATGCACCTTAGTGGAG-TTTT-TGATAAACATCGCAATAGTCATGCACCTTATCGGC
1 CAATAGTCATGCACCTTAGCGGAGTTTTTATAATAAACACCGCAATAGCCATGCACCTTATCGGC
4305294 GTTTTTGTAATAAACGTCA
66 GTTTTTGTAATAAACGTCA
*
4305313 CAATTGTCATGCACCTTAGCGG
1 CAATAGTCATGCACCTTAGCGG
4305335 CAACAGTCAT
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
81 1 0.01
82 62 0.69
83 6 0.07
84 21 0.23
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (84 bp):
CAATAGTCATGCACCTTAGCGGAGTTTTTATAATAAACACCGCAATAGCCATGCACCTTATCGGC
GTTTTTGTAATAAACGTCA
Found at i:4305394 original size:62 final size:64
Alignment explanation
Indices: 4305270--4305398 Score: 201
Period size: 62 Copynumber: 2.0 Consensus size: 64
4305260 GATAAACATC
* * *
4305270 GCAATAGTCATGCACCTTATCGGCGTTTTTGTAATAAACGTCACAATTGTCATGCACCTTAGCG
1 GCAACAGTCATGCACCTTAGCGGCGTTTTTGTAATAAACGTCACAATTGTCATGCACATTAGCG
4305334 GCAACAGTCATGCACCTTAGCGGCGTTTTT-T-ATAAACGTCACAATAT-TCATGCACATTAGCG
1 GCAACAGTCATGCACCTTAGCGGCGTTTTTGTAATAAACGTCACAAT-TGTCATGCACATTAGCG
4305396 GCA
1 GCA
4305399 TTTTTGTAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
62 31 0.51
63 2 0.03
64 28 0.46
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (64 bp):
GCAACAGTCATGCACCTTAGCGGCGTTTTTGTAATAAACGTCACAATTGTCATGCACATTAGCG
Found at i:4305426 original size:104 final size:104
Alignment explanation
Indices: 4305235--4305435 Score: 278
Period size: 104 Copynumber: 1.9 Consensus size: 104
4305225 ACTCTGTAAT
* * * * *
4305235 AGTCATGCACCTTAGTGGAGTTTTTGATAAACATCGCAATAGTCATGCACCTTATCGGCGTTTTT
1 AGTCATGCACCTTAGCGGAGTTTTTGATAAACATCACAATAGTCATGCACATTAGCGGCATTTTT
*
4305300 GTAATAAACGTCACAATTGTCAT-GCACCTTAGCGGCAAC
66 GTAATAAACGTCACAATAGTCATGGC-CCTTAGCGGCAAC
* * * *
4305339 AGTCATGCACCTTAGCGGCGTTTTTTATAAACGTCACAATATTCATGCACATTAGCGGCATTTTT
1 AGTCATGCACCTTAGCGGAGTTTTTGATAAACATCACAATAGTCATGCACATTAGCGGCATTTTT
* *
4305404 GTAATAAATGTCGCAATAGTCATGGCCCTTAG
66 GTAATAAACGTCACAATAGTCATGGCCCTTAG
4305436 TGGCGTTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
104 82 0.98
105 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (104 bp):
AGTCATGCACCTTAGCGGAGTTTTTGATAAACATCACAATAGTCATGCACATTAGCGGCATTTTT
GTAATAAACGTCACAATAGTCATGGCCCTTAGCGGCAAC
Found at i:4305427 original size:42 final size:40
Alignment explanation
Indices: 4305334--4305427 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
4305324 CACCTTAGCG
* * *
4305334 GCAACAGTCATGCACCTTAGCGGCGTTTTTTATAAACGTC
1 GCAATAGTCATGCACATTAGCGGCATTTTTTATAAACGTC
* * *
4305374 ACAATATTCATGCACATTAGCGGCATTTTTGTAATAAATGTC
1 GCAATAGTCATGCACATTAGCGGCATTTTT-T-ATAAACGTC
4305416 GCAATAGTCATG
1 GCAATAGTCATG
4305428 GCCCTTAGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 25 0.57
41 1 0.02
42 18 0.41
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (40 bp):
GCAATAGTCATGCACATTAGCGGCATTTTTTATAAACGTC
Found at i:4305445 original size:42 final size:42
Alignment explanation
Indices: 4305339--4305466 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
4305329 TAGCGGCAAC
*
4305339 AGTCATGCACCTTAGCGGCGTTTTT-T-ATAAACGTCACAAT
1 AGTCATGCACCTTAGCGGCGTTTTTGTAATAAATGTCACAAT
* * * *
4305379 ATTCATGCACATTAGCGGCATTTTTGTAATAAATGTCGCAAT
1 AGTCATGCACCTTAGCGGCGTTTTTGTAATAAATGTCACAAT
* * * *
4305421 AGTCATGGC-CCTTAGTGGCGTTTTTGTAGTAATTGCCACAAT
1 AGTCAT-GCACCTTAGCGGCGTTTTTGTAATAAATGTCACAAT
4305463 AGTC
1 AGTC
4305467 GCAATAGTCA
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 22 0.31
41 1 0.01
42 47 0.65
43 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (42 bp):
AGTCATGCACCTTAGCGGCGTTTTTGTAATAAATGTCACAAT
Found at i:4305641 original size:197 final size:197
Alignment explanation
Indices: 4305268--4305642 Score: 504
Period size: 197 Copynumber: 1.9 Consensus size: 197
4305258 TTGATAAACA
** *
4305268 TCGCAATAGTCATGCACCTTATCGGCGTTTTTGTAATAAACGTCACAATTGTCATGCACCTTAGC
1 TCGCAATAGTCATGCACCTTATCAACGTTTTTGTAATAAACGACACAATTGTCATGCACCTTAGC
*
4305333 GGCAACAGTCATGCACCTTAGCGGCGTTTTTTATAAACGTCACAATATTCATGCACATTAGCGGC
66 GGCAACAGTCATGCACCTTAGCGGAGTTTTTTATAAACGTCACAATATTCATGCACATTAGCGGC
* **
4305398 ATTTTTGTAATAAATGTCGCAATAGTCATGGCCCTTAGTGGCGTTTTTGTAGTAATTGCCACAAT
131 ATTTTTGTAATAAACGTCGCAATAGTCATGGCCCTTAGCAGCGTTTTTGTAGTAATTGCCACAAT
4305463 AG
196 AG
* *** * * *
4305465 TCGCAATAGTCATGCACCTTATCAACTTTTTTGTAATAAACGACGTGATTGTTATGCATCTTAGT
1 TCGCAATAGTCATGCACCTTATCAACGTTTTTGTAATAAACGACACAATTGTCATGCACCTTAGC
* * * *
4305530 GGCAATAGTCCTGCACCTTAGCGGAGTTTTTTATAAACG-CAGCAATATTCATGTACTTTAGCGG
66 GGCAACAGTCATGCACCTTAGCGGAGTTTTTTATAAACGTCA-CAATATTCATGCACATTAGCGG
** * *
4305594 TGTTTTTGTAATAAACGTTGTAATAGGT-AT-GCTCCTTAGCAGCGTTTTT
130 CATTTTTGTAATAAACGTCGCAATA-GTCATGGC-CCTTAGCAGCGTTTTT
4305643 ATAATAAATG
Statistics
Matches: 153, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
196 4 0.03
197 147 0.96
198 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (197 bp):
TCGCAATAGTCATGCACCTTATCAACGTTTTTGTAATAAACGACACAATTGTCATGCACCTTAGC
GGCAACAGTCATGCACCTTAGCGGAGTTTTTTATAAACGTCACAATATTCATGCACATTAGCGGC
ATTTTTGTAATAAACGTCGCAATAGTCATGGCCCTTAGCAGCGTTTTTGTAGTAATTGCCACAAT
AG
Found at i:4305700 original size:81 final size:81
Alignment explanation
Indices: 4305622--4305814 Score: 190
Period size: 81 Copynumber: 2.4 Consensus size: 81
4305612 TGTAATAGGT
* * * * * **
4305622 ATGCTCCTTAGCAGCGTTTTTATAATAAATGACGTGATAGTCATGCACCTTAGGGGCGTTTTTAT
1 ATGCACCTTAACAGCATTTTTATAATAAATGACGCGATAATCATGCACCTTAACGGCGTTTTTAT
4305687 AAACGCCGCAATAGTC
66 AAACGCCGCAATAGTC
* * **
4305703 ATGCACCTTAACGGCATTTTTTTAATAAATGTTGCGATAATCATGCACCTTAACGGCGTTTTTGT
1 ATGCACCTTAACAGCATTTTTATAATAAATGACGCGATAATCATGCACCTTAACGGCG-TTTT-T
* ** * *
4305768 AATAAGCGATGCGATAGTA
64 -ATAAACGCCGCAATAGTC
* *
4305787 ATGCACCTTAACAG-TTTTTTGTAATAAA
1 ATGCACCTTAACAGCATTTTTATAATAAA
4305815 CTTCGTGACA
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
81 47 0.52
82 4 0.04
83 13 0.14
84 26 0.29
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (81 bp):
ATGCACCTTAACAGCATTTTTATAATAAATGACGCGATAATCATGCACCTTAACGGCGTTTTTAT
AAACGCCGCAATAGTC
Found at i:4305701 original size:39 final size:42
Alignment explanation
Indices: 4305531--4305865 Score: 189
Period size: 42 Copynumber: 8.1 Consensus size: 42
4305521 CATCTTAGTG
* * *
4305531 GCAATAGTCCTGCACCTTAGCGGAGTTTTT-T-ATAAACGCA
1 GCAATAGTCATGCACCTTAGCGGCGTTTTTATAATAAACGCC
* * * * * **
4305571 GCAATATTCATGTACTTTAGCGGTGTTTTTGTAATAAACGTT
1 GCAATAGTCATGCACCTTAGCGGCGTTTTTATAATAAACGCC
* * * * *
4305613 GTAATAGGT-ATGCTCCTTAGCAGCGTTTTTATAATAAATGAC
1 GCAATA-GTCATGCACCTTAGCGGCGTTTTTATAATAAACGCC
** *
4305655 GTGATAGTCATGCACCTTAGGGGCG-TTTT-T-ATAAACGCC
1 GCAATAGTCATGCACCTTAGCGGCGTTTTTATAATAAACGCC
* * * * **
4305694 GCAATAGTCATGCACCTTAACGGCATTTTTTTAATAAATGTT
1 GCAATAGTCATGCACCTTAGCGGCGTTTTTATAATAAACGCC
* * * * * **
4305736 GCGATAATCATGCACCTTAACGGCGTTTTTGTAATAAGCGAT
1 GCAATAGTCATGCACCTTAGCGGCGTTTTTATAATAAACGCC
* * * * * * **
4305778 GCGATAGTAATGCACCTTAACAG-TTTTTTGTAATAAACTTC
1 GCAATAGTCATGCACCTTAGCGGCGTTTTTATAATAAACGCC
** * * * * * *
4305819 GTGACAATCATGTATCTTAGTGGCGTTTTTTTAATAAACGCC
1 GCAATAGTCATGCACCTTAGCGGCGTTTTTATAATAAACGCC
4305861 GCAAT
1 GCAAT
4305866 TTTACAATCC
Statistics
Matches: 224, Mismatches: 63, Indels: 14
0.74 0.21 0.05
Matches are distributed among these distances:
39 27 0.12
40 30 0.13
41 35 0.16
42 131 0.58
43 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (42 bp):
GCAATAGTCATGCACCTTAGCGGCGTTTTTATAATAAACGCC
Found at i:4305754 original size:123 final size:124
Alignment explanation
Indices: 4305534--4305796 Score: 287
Period size: 123 Copynumber: 2.1 Consensus size: 124
4305524 CTTAGTGGCA
* * * * * **
4305534 ATAGTCCTGCACCTTAGCGGAGTTTTTTATAAACGCAGCAATATTCATGTACTTTAGCGGTGTTT
1 ATAGTCATGCACCTTAGCGGAGTTTTTTATAAACGCAGCAATAGTCATGCACCTTAACGGCATTT
* * * * * *
4305599 TTGTAATAAACGTTGTAATAGGTATGCTCCTTAGCAGCGTTTTTATAATAAATGACGTG
66 TTGTAATAAACGTTGCAATAGATATGCACCTTAACAGCGTTTTTATAATAAACGACGCG
* * *
4305658 ATAGTCATGCACCTTAGGGGCG-TTTTTATAAACGCCGCAATAGTCATGCACCTTAACGGCATTT
1 ATAGTCATGCACCTTAGCGGAGTTTTTTATAAACGCAGCAATAGTCATGCACCTTAACGGCATTT
* * * * * * *
4305722 TTTTAATAAATGTTGCGATA-ATCATGCACCTTAACGGCGTTTTTGTAATAAGCGATGCG
66 TTGTAATAAACGTTGCAATAGAT-ATGCACCTTAACAGCGTTTTTATAATAAACGACGCG
*
4305781 ATAGTAATGCACCTTA
1 ATAGTCATGCACCTTA
4305797 ACAGTTTTTT
Statistics
Matches: 114, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
122 1 0.01
123 94 0.82
124 19 0.17
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (124 bp):
ATAGTCATGCACCTTAGCGGAGTTTTTTATAAACGCAGCAATAGTCATGCACCTTAACGGCATTT
TTGTAATAAACGTTGCAATAGATATGCACCTTAACAGCGTTTTTATAATAAACGACGCG
Found at i:4308911 original size:36 final size:36
Alignment explanation
Indices: 4308811--4309023 Score: 259
Period size: 36 Copynumber: 6.0 Consensus size: 36
4308801 TGAATAAGAA
*
4308811 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
1 GAACGGAAGGAGGCATCGACACTTCCGATTCAAGTC
* * *
4308847 AAACGGAAGGAGACGTC-ACACTTCCGATTCAAGTC
1 GAACGGAAGGAGGCATCGACACTTCCGATTCAAGTC
* * * *
4308882 GAACGGAATGTGGCATCAACACTTTCGATTCAAGTC
1 GAACGGAAGGAGGCATCGACACTTCCGATTCAAGTC
* *
4308918 GAACGGAAGGAAGCATCGACACTTCTGATTCAAGTC
1 GAACGGAAGGAGGCATCGACACTTCCGATTCAAGTC
* * * *
4308954 GAACGGAAGGAAGCATTGATACTTCTGATTCAAGTC
1 GAACGGAAGGAGGCATCGACACTTCCGATTCAAGTC
* * *
4308990 GACCGGAAGGAAGCATCG-CACTTCTGATTCAAGT
1 GAACGGAAGGAGGCATCGACACTTCCGATTCAAGT
4309024 TGAATAGAAT
Statistics
Matches: 155, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
35 45 0.29
36 110 0.71
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (36 bp):
GAACGGAAGGAGGCATCGACACTTCCGATTCAAGTC
Found at i:4309012 original size:107 final size:107
Alignment explanation
Indices: 4308811--4309023 Score: 279
Period size: 107 Copynumber: 2.0 Consensus size: 107
4308801 TGAATAAGAA
4308811 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTCAAACGGAAGGAGACGTCACACTTCCGATT
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTCAAACGGAAGGAGACGTCACACTTCCGATT
* **
4308876 CAAGTCGAACGGAATGTGGCATCAACACTT-TCGATTCAAGTC
66 CAAGTCGAACGGAAGGAAGCATCAACACTTCT-GATTCAAGTC
* * * * * *
4308918 GAACGGAAGGAAGCATCGACACTTCTGATTCAAGTCGAACGGAAGGA-AGCATTGATACTTCTGA
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTCAAACGGAAGGAGA-C-GTCACACTTCCGA
* *
4308982 TTCAAGTCGACCGGAAGGAAGCATC-GCACTTCTGATTCAAGT
64 TTCAAGTCGAACGGAAGGAAGCATCAACACTTCTGATTCAAGT
4309024 TGAATAGAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
106 1 0.01
107 60 0.65
108 31 0.34
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (107 bp):
GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTCAAACGGAAGGAGACGTCACACTTCCGATT
CAAGTCGAACGGAAGGAAGCATCAACACTTCTGATTCAAGTC
Found at i:4311462 original size:19 final size:19
Alignment explanation
Indices: 4311434--4311506 Score: 94
Period size: 19 Copynumber: 3.8 Consensus size: 19
4311424 TAATTGGATG
*
4311434 ACCGGCTTGACCGGTCCAA
1 ACCGGTTTGACCGGTCCAA
*
4311453 ACCGGTTTGACCGGTCTAA
1 ACCGGTTTGACCGGTCCAA
* *
4311472 ACCGGTTTGACTGGTCCGA
1 ACCGGTTTGACCGGTCCAA
4311491 ACCGAG-TTGACCGGTC
1 ACCG-GTTTGACCGGTC
4311507 TGACCCGACC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 46 0.98
20 1 0.02
ACGTcount: A:0.19, C:0.30, G:0.29, T:0.22
Consensus pattern (19 bp):
ACCGGTTTGACCGGTCCAA
Found at i:4311488 original size:38 final size:38
Alignment explanation
Indices: 4311434--4311507 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
4311424 TAATTGGATG
4311434 ACCGGCTTGACCGGTCCAAACCG-GTTTGACCGGTCTAA
1 ACCGGCTTGACCGGTCCAAACCGAG-TTGACCGGTCTAA
* * *
4311472 ACCGGTTTGACTGGTCCGAACCGAGTTGACCGGTCT
1 ACCGGCTTGACCGGTCCAAACCGAGTTGACCGGTCT
4311508 GACCCGACCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 31 0.97
39 1 0.03
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (38 bp):
ACCGGCTTGACCGGTCCAAACCGAGTTGACCGGTCTAA
Found at i:4311514 original size:19 final size:20
Alignment explanation
Indices: 4311440--4311514 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 20
4311430 GATGACCGGC
**
4311440 TTGACCGGTCCAAACCG-GT
1 TTGACCGGTCTGAACCGAGT
*
4311459 TTGACCGGTCTAAACCG-GT
1 TTGACCGGTCTGAACCGAGT
* *
4311478 TTGACTGGTCCGAACCGAG-
1 TTGACCGGTCTGAACCGAGT
*
4311497 TTGACCGGTCTGACCCGA
1 TTGACCGGTCTGAACCGA
4311515 CCCGACCCGG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 47 0.98
20 1 0.02
ACGTcount: A:0.20, C:0.29, G:0.28, T:0.23
Consensus pattern (20 bp):
TTGACCGGTCTGAACCGAGT
Found at i:4311557 original size:29 final size:28
Alignment explanation
Indices: 4311523--4311658 Score: 155
Period size: 29 Copynumber: 4.7 Consensus size: 28
4311513 GACCCGACCC
4311523 GGTGACATTCTGGGAATTTTTGTGAAAAA
1 GGTGACATTCTGGGAATTTTT-TGAAAAA
* * *
4311552 TGTGACATTCTGTGAAATATTTTGAAAAA
1 GGTGACATTCTG-GGAATTTTTTGAAAAA
* *
4311581 GGGGACATTCTGGGAAATATTTTGAAAAA
1 GGTGACATTCTGGG-AATTTTTTGAAAAA
*
4311610 GGTGATATTCTGGGAATTATTTTGAAAAA
1 GGTGACATTCTGGGAATT-TTTTGAAAAA
* * *
4311639 TGTGACATTTTGGAAATTTT
1 GGTGACATTCTGGGAATTTT
4311659 CGAATGTGGA
Statistics
Matches: 91, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
28 6 0.07
29 78 0.86
30 7 0.08
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.37
Consensus pattern (28 bp):
GGTGACATTCTGGGAATTTTTTGAAAAA
Found at i:4318945 original size:10 final size:10
Alignment explanation
Indices: 4318932--4318980 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
4318922 GACCGGTCCA
4318932 AACCGGTCTG
1 AACCGGTCTG
*
4318942 AACCGGTTTG
1 AACCGGTCTG
*
4318952 -ACCGGTCCG
1 AACCGGTCTG
4318961 AACCGGGT-TG
1 AACC-GGTCTG
4318971 -ACCGGTCTG
1 AACCGGTCTG
4318980 A
1 A
4318981 CCCGACTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
8 3 0.10
9 12 0.39
10 13 0.42
11 3 0.10
ACGTcount: A:0.18, C:0.29, G:0.33, T:0.20
Consensus pattern (10 bp):
AACCGGTCTG
Found at i:4318955 original size:19 final size:19
Alignment explanation
Indices: 4318933--4318980 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
4318923 ACCGGTCCAA
*
4318933 ACCGGTCTGAACCGGTTTG
1 ACCGGTCTGAACCGGGTTG
*
4318952 ACCGGTCCGAACCGGGTTG
1 ACCGGTCTGAACCGGGTTG
4318971 ACCGGTCTGA
1 ACCGGTCTGA
4318981 CCCGACTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.17, C:0.29, G:0.33, T:0.21
Consensus pattern (19 bp):
ACCGGTCTGAACCGGGTTG
Found at i:4318956 original size:29 final size:28
Alignment explanation
Indices: 4318909--4318982 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
4318899 GGTGTTAATT
*
4318909 GGTTGACCGGCTTGACCGGTCCAAACC-
1 GGTTGACCGGTTTGACCGGTCCAAACCG
*
4318936 GGTCTGAACCGGTTTGACCGGTCCGAACCG
1 GGT-TG-ACCGGTTTGACCGGTCCAAACCG
*
4318966 GGTTGACCGGTCTGACC
1 GGTTGACCGGTTTGACC
4318983 CGACTAGACC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 3 0.07
28 13 0.32
29 22 0.54
30 3 0.07
ACGTcount: A:0.16, C:0.31, G:0.32, T:0.20
Consensus pattern (28 bp):
GGTTGACCGGTTTGACCGGTCCAAACCG
Found at i:4319067 original size:29 final size:29
Alignment explanation
Indices: 4319011--4319174 Score: 163
Period size: 29 Copynumber: 5.6 Consensus size: 29
4319001 GACCCGACCC
* * *
4319011 GGTGATATTCTG-GGAATTTTTGTGAAAAA
1 GGTGACATTCTGAGAAATATTT-TGAAAAA
** *
4319040 TATGACATTCTGAGAAATATTTTTAAAAA
1 GGTGACATTCTGAGAAATATTTTGAAAAA
*
4319069 GGTGACATTCTGGGAAATATTTTGAAAAA
1 GGTGACATTCTGAGAAATATTTTGAAAAA
4319098 GGTGACATTCT-AGGAAATATTTTGAAAAA
1 GGTGACATTCTGA-GAAATATTTTGAAAAA
* * * *
4319127 TGTGACATTCTGGGAATTATTTTAAAACAAA
1 GGTGACATTCTGAGAAATATTTT-GAA-AAA
*
4319158 GGTGACATTTTG-GAAAT
1 GGTGACATTCTGAGAAAT
4319175 TTTCGAACGT
Statistics
Matches: 112, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
29 86 0.77
30 13 0.12
31 13 0.12
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.35
Consensus pattern (29 bp):
GGTGACATTCTGAGAAATATTTTGAAAAA
Found at i:4319104 original size:58 final size:58
Alignment explanation
Indices: 4319011--4319174 Score: 190
Period size: 58 Copynumber: 2.8 Consensus size: 58
4319001 GACCCGACCC
* * ** *
4319011 GGTGATATTCTGGG-AATTTTTGTGAAAAATATGACATTCTGAGAAATATTTTTAAAAA
1 GGTGACATTCTGGGAAATATTT-TGAAAAAGGTGACATTCTGAGAAATATTTTGAAAAA
4319069 GGTGACATTCTGGGAAATATTTTGAAAAAGGTGACATTCT-AGGAAATATTTTGAAAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAAGGTGACATTCTGA-GAAATATTTTGAAAAA
* * * *
4319127 TGTGACATTCTGGGAATTATTTTAAAACAAAGGTGACATTTTG-GAAAT
1 GGTGACATTCTGGGAAATATTTT-GAA-AAAGGTGACATTCTGAGAAAT
4319175 TTTCGAACGT
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
57 1 0.01
58 65 0.71
59 13 0.14
60 13 0.14
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.35
Consensus pattern (58 bp):
GGTGACATTCTGGGAAATATTTTGAAAAAGGTGACATTCTGAGAAATATTTTGAAAAA
Found at i:4329923 original size:15 final size:15
Alignment explanation
Indices: 4329903--4329939 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
4329893 TGAGACATTA
*
4329903 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
4329918 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
4329933 CCCGCCC
1 CCCGCCC
4329940 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:4332354 original size:2 final size:2
Alignment explanation
Indices: 4332347--4332371 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4332337 TACTTTGATG
4332347 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4332372 TTTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4338627 original size:36 final size:35
Alignment explanation
Indices: 4338582--4338650 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 35
4338572 AACCATTATT
4338582 TCTCTTGAGACAGTTTCCCTTGAAACAAA-CTTTGTC
1 TCTCTTGAGACAGTTTCCCTT-AAA-AAACCTTTGTC
4338618 TCTCTTGAGACAGTTTCCCTTAAAAAACCTTTG
1 TCTCTTGAGACAGTTTCCCTTAAAAAACCTTTG
4338651 AAATTGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 3 0.09
35 8 0.25
36 21 0.66
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (35 bp):
TCTCTTGAGACAGTTTCCCTTAAAAAACCTTTGTC
Found at i:4339655 original size:106 final size:106
Alignment explanation
Indices: 4339501--4339926 Score: 665
Period size: 106 Copynumber: 4.0 Consensus size: 106
4339491 TCGCGCCACC
* * *
4339501 CGAGACAATACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAAT
4339566 TTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
66 TTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
* *
4339607 CAAGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAAT
* **
4339672 TTCAGAGCCAATTTCAACTTCACAACGAAGGGCATTGGACT
66 TTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
*
4339713 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAAT
* * *
4339778 TTCAGAGCCAATTTCAACTTCACAGCGAAGGGTATTGGACT
66 TTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
* * * *
4339819 CGAGACAGCACAAGTTCATCTCCACAACGAAGGGACGACTGGTTGTCAACAAATAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAAT
** *
4339884 TTCAGAA-CCAATTTCAACTTCACGGCGGAGGATATTGGACT
66 TTCA-AAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
4339925 CG
1 CG
4339927 GAACAATACT
Statistics
Matches: 297, Mismatches: 22, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
106 296 1.00
107 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAAT
TTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
Found at i:4341206 original size:17 final size:18
Alignment explanation
Indices: 4341180--4341219 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4341170 ATTATATGGA
4341180 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
4341196 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
4341214 TATTAT
1 TATTAT
4341220 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:4341230 original size:2 final size:2
Alignment explanation
Indices: 4341223--4341249 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4341213 TTATTATACG
4341223 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4341250 TAAATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4341811 original size:2 final size:2
Alignment explanation
Indices: 4341804--4341844 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4341794 TACTTTGATG
4341804 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4341845 TCCTTTTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4344585 original size:2 final size:2
Alignment explanation
Indices: 4344578--4344634 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
4344568 TATAAGCTTT
4344578 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
4344620 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
4344635 CATCACTTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4346644 original size:2 final size:2
Alignment explanation
Indices: 4346637--4346686 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
4346627 TGTATTGTAT
4346637 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
4346679 TA TA TA TA
1 TA TA TA TA
4346687 CTTACACGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4346882 original size:5 final size:5
Alignment explanation
Indices: 4346872--4346914 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
4346862 AAGATGAAGT
*
4346872 AAATA AAATA AAATA AAATA AAATA AAACA TAAAT- AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA -AAATA AAATA AAA
4346915 CTCAACACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.12
5 27 0.79
6 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:4348664 original size:3 final size:3
Alignment explanation
Indices: 4348656--4348684 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4348646 TAAATTTCAA
4348656 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4348685 ATTAAAAATA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4349131 original size:134 final size:134
Alignment explanation
Indices: 4348891--4349222 Score: 475
Period size: 134 Copynumber: 2.5 Consensus size: 134
4348881 GTCGTCTAAA
* * *
4348891 GGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGATGACACGGCTCATACGTGATGAA
1 GGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCAGGGGATGACACGGCTCATACGTGATGAA
* * * * * *
4348956 GAGTTCTGGCCATCTTTAGGAATGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGATTATC
66 GACTTCTAGCCATCTTTAGAAAGGGCGATAACACGGTTCCTACGCGATGAGGACGGCTGATTATC
*
4349021 TATG
131 TAGG
*
4349025 GGTGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGGATGACACGGCTCATACGTGATGAA
1 GGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCAGGGGATGACACGGCTCATACGTGATGAA
* * * * *
4349090 GACTTCTAGTCATTTTTAGAAAGGGCGATAACACGGTTCCTACGTGATGAGGACGTCTGGTTATC
66 GACTTCTAGCCATCTTTAGAAAGGGCGATAACACGGTTCCTACGCGATGAGGACGGCTGATTATC
4349155 TAGG
131 TAGG
* * * * *
4349159 GGTAACACGACTCCTACGCGATGAAGAGATCTGGTCAGGGGATGACACTGCTCCTACGTGATGA
1 GGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCAGGGGATGACACGGCTCATACGTGATGA
4349223 GGACGACTGG
Statistics
Matches: 176, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
134 176 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (134 bp):
GGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCAGGGGATGACACGGCTCATACGTGATGAA
GACTTCTAGCCATCTTTAGAAAGGGCGATAACACGGTTCCTACGCGATGAGGACGGCTGATTATC
TAGG
Found at i:4349182 original size:43 final size:43
Alignment explanation
Indices: 4349111--4349238 Score: 124
Period size: 43 Copynumber: 3.0 Consensus size: 43
4349101 ATTTTTAGAA
*
4349111 AGGGCGATAACACGGTTCCTACGTGATGAGGACGTCTGGTTATCT
1 AGGG-GATAACAC-GCTCCTACGTGATGAGGACGTCTGGTTATCT
* *
4349156 AGGGG-TAACACGACTCCTACGCGATGAAGA-GATCTGG---TC-
1 AGGGGATAACACG-CTCCTACGTGATGAGGACG-TCTGGTTATCT
* *
4349195 AGGGGATGACACTGCTCCTACGTGATGAGGACGACTGGTTATCT
1 AGGGGATAACAC-GCTCCTACGTGATGAGGACGTCTGGTTATCT
4349239 TTAGTGATTG
Statistics
Matches: 67, Mismatches: 7, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
39 5 0.07
40 26 0.39
41 2 0.03
42 2 0.03
43 27 0.40
44 1 0.01
45 4 0.06
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.23
Consensus pattern (43 bp):
AGGGGATAACACGCTCCTACGTGATGAGGACGTCTGGTTATCT
Found at i:4349233 original size:40 final size:40
Alignment explanation
Indices: 4349118--4349233 Score: 103
Period size: 40 Copynumber: 2.8 Consensus size: 40
4349108 GAAAGGGCGA
** *
4349118 TAACACGGTTCCTACGTGATGAGGACGTCTGGTTATCTAGGGG
1 TAACACGACTCCTACGTGATGAGGACGACTGG---TCTAGGGG
* *
4349161 TAACACGACTCCTACGCGATGAAGA-GATCTGGTC-AGGGG
1 TAACACGACTCCTACGTGATGAGGACGA-CTGGTCTAGGGG
*
4349200 ATGACACTG-CTCCTACGTGATGAGGACGACTGGT
1 -TAACAC-GACTCCTACGTGATGAGGACGACTGGT
4349234 TATCTTTAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
39 5 0.08
40 27 0.44
41 3 0.05
42 1 0.02
43 25 0.41
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (40 bp):
TAACACGACTCCTACGTGATGAGGACGACTGGTCTAGGGG
Found at i:4349599 original size:36 final size:35
Alignment explanation
Indices: 4349519--4349829 Score: 184
Period size: 36 Copynumber: 9.0 Consensus size: 35
4349509 GTATTATGAG
* * *
4349519 GGAAAATGTCTCAAGTGAGACGAAATTTG-TTTT-
1 GGAAATTGTCTCAAGCGAGACAAAATTTGTTTTTA
*
4349552 -GAAATTGTCTCAAACGAGACAAAATTTGTTTTTAA
1 GGAAATTGTCTCAAGCGAGACAAAATTTGTTTTT-A
* *
4349587 GGAAATTGTCTCAAGTGAGACAAAATTTATTTTTA
1 GGAAATTGTCTCAAGCGAGACAAAATTTGTTTTTA
*
4349622 GAGAAATTGTCTCAAGCGAGACAAAATTTGTTTAT-
1 G-GAAATTGTCTCAAGCGAGACAAAATTTGTTTTTA
** * * *
4349657 GAGAAAACGATCTCAAGTGAGATC-AACTTTG-TTTAA
1 G-GAAATTG-TCTCAAGCGAGA-CAAAATTTGTTTTTA
** * *
4349693 TGTGAAA------CAA---ATTCGAAATTTGTATTTCAAA
1 -G-GAAATTGTCTCAAGCGAGACAAAATTTGT-TTT--TA
* *
4349724 GGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTTCA
1 GG-AAATTGTCTCAAGCGAGACAAAATTTGTTTTT-A
** * *
4349761 ATAAATTGTCTCAAACGAGACAAAATTTGATTTTA
1 GGAAATTGTCTCAAGCGAGACAAAATTTGTTTTTA
* * *
4349796 GAAAACTGTCTCAAGCGAGACAAGATTTGTTTTT
1 GGAAATTGTCTCAAGCGAGACAAAATTTGTTTTT
4349830 CAAAAGAAGC
Statistics
Matches: 218, Mismatches: 35, Indels: 48
0.72 0.12 0.16
Matches are distributed among these distances:
26 1 0.00
27 7 0.03
29 4 0.02
30 7 0.03
31 2 0.01
32 24 0.11
33 4 0.02
35 40 0.18
36 108 0.50
37 7 0.03
38 3 0.01
39 11 0.05
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.33
Consensus pattern (35 bp):
GGAAATTGTCTCAAGCGAGACAAAATTTGTTTTTA
Found at i:4349650 original size:72 final size:68
Alignment explanation
Indices: 4349519--4349828 Score: 237
Period size: 72 Copynumber: 4.5 Consensus size: 68
4349509 GTATTATGAG
*
4349519 GGAAAATGTCTCAAGTGAGACGAAATTTGTTTTGAAATTGTCTCAAACGAGACAAAATTTGTTTT
1 GGAAAATGTCTCAAGTGAGACAAAATTTGTTTTGAAATTGTCTCAAACGAGACAAAATTTGTTTT
4349584 TAA
66 TAA
* * *
4349587 GGAAATTGTCTCAAGTGAGACAAAATTTATTTTTAGAGAAATTGTCTCAAGCGAGACAAAATTTG
1 GGAAAATGTCTCAAGTGAGACAAAATTT-GTTTT---GAAATTGTCTCAAACGAGACAAAATTTG
* *
4349652 TTTATGA
62 TTTTTAA
* * * * *
4349659 -GAAAACGATCTCAAGTGAGATC-AACTTTG-TTT--AA-TG--TGAAAC-AAATTCGAAATTTG
1 GGAAAATG-TCTCAAGTGAGA-CAAAATTTGTTTTGAAATTGTCTCAAACGAGA--CAAAATTTG
*
4349715 TATTTCAAA
62 T-TTT-TAA
* * *
4349724 GGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTTCAATAAATTGTCTCAAACGAGACAAAATTT
1 GG-AAAATGTCTCAAGTGAGACAAAATTTG-TTTT---GAAATTGTCTCAAACGAGACAAAATTT
*
4349789 GATTTT-A
61 GTTTTTAA
* *
4349796 -GAAAACTGTCTCAAGCGAGACAAGATTTGTTTT
1 GGAAAA-TGTCTCAAGTGAGACAAAATTTGTTTT
4349829 TCAAAAGAAG
Statistics
Matches: 190, Mismatches: 27, Indels: 48
0.72 0.10 0.18
Matches are distributed among these distances:
61 2 0.01
62 4 0.02
63 9 0.05
64 4 0.02
65 4 0.02
66 18 0.09
67 5 0.03
68 29 0.15
69 4 0.02
70 11 0.06
71 27 0.14
72 50 0.26
73 3 0.02
74 5 0.03
75 8 0.04
76 5 0.03
77 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.33
Consensus pattern (68 bp):
GGAAAATGTCTCAAGTGAGACAAAATTTGTTTTGAAATTGTCTCAAACGAGACAAAATTTGTTTT
TAA
Found at i:4349815 original size:35 final size:36
Alignment explanation
Indices: 4349725--4349866 Score: 144
Period size: 36 Copynumber: 3.9 Consensus size: 36
4349715 TATTTCAAAG
* *
4349725 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTTCA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTCA
* * *
4349761 -ATAAATTGTCTCAAACGAGACAAAATTTGATTTT-A
1 GA-AAACTGTCTCAAGCGAGACAAAATTTGTTTTTCA
*
4349796 GAAAACTGTCTCAAGCGAGACAAGATTTGTTTTTCA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTCA
* * * *
4349832 AAAGAAGCTGTCTCTAGCAAGACAACATTTTGTTT
1 GAA-AA-CTGTCTCAAGCGAGACAA-AATTTGTTT
4349867 CGAGAGAAAC
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
35 30 0.34
36 32 0.37
37 2 0.02
38 16 0.18
39 7 0.08
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (36 bp):
GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTCA
Found at i:4350206 original size:16 final size:16
Alignment explanation
Indices: 4350171--4350248 Score: 111
Period size: 16 Copynumber: 4.8 Consensus size: 16
4350161 TTTATGTATC
4350171 ATGCATGTATGTGTATGT
1 ATGCATGTA--TGTATGT
*
4350189 ATGCATGTATGCATGT
1 ATGCATGTATGTATGT
4350205 ATGCATGTATGTATGT
1 ATGCATGTATGTATGT
*
4350221 ATGTATGTATGTATGT
1 ATGCATGTATGTATGT
*
4350237 ATGTATGTATGT
1 ATGCATGTATGT
4350249 GTTGATGTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
16 48 0.84
18 9 0.16
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (16 bp):
ATGCATGTATGTATGT
Found at i:4350256 original size:16 final size:17
Alignment explanation
Indices: 4350175--4350260 Score: 81
Period size: 16 Copynumber: 5.2 Consensus size: 17
4350165 TGTATCATGC
*
4350175 ATGTATGTGTATGTATGC
1 ATGTATGTGT-TGTATGT
** *
4350193 ATGTATG-CATGTATGC
1 ATGTATGTGTTGTATGT
*
4350209 ATGTATGT-ATGTATGT
1 ATGTATGTGTTGTATGT
*
4350225 ATGTATGT-ATGTATGT
1 ATGTATGTGTTGTATGT
4350241 ATGTATGTGTTG-ATGT
1 ATGTATGTGTTGTATGT
4350257 ATGT
1 ATGT
4350261 TTTTCTCGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
16 53 0.85
17 2 0.03
18 7 0.11
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (17 bp):
ATGTATGTGTTGTATGT
Found at i:4350260 original size:4 final size:4
Alignment explanation
Indices: 4350182--4350248 Score: 107
Period size: 4 Copynumber: 16.8 Consensus size: 4
4350172 TGCATGTATG
* * *
4350182 TGTA TGTA TGCA TGTA TGCA TGTA TGCA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
4350230 TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGT
4350249 GTTGATGTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.24, C:0.04, G:0.25, T:0.46
Consensus pattern (4 bp):
TGTA
Found at i:4351476 original size:12 final size:11
Alignment explanation
Indices: 4351440--4351541 Score: 63
Period size: 11 Copynumber: 9.1 Consensus size: 11
4351430 TCTTTATCTT
4351440 TTTGCTTTTGTC
1 TTTGCTTTT-TC
4351452 -TT-CTTTTTC
1 TTTGCTTTTTC
4351461 TTTGCTTTTTC
1 TTTGCTTTTTC
4351472 GTTTGCTATTTTTCC
1 -TTTGC--TTTTT-C
*
4351487 TTTGATTTTTC
1 TTTGCTTTTTC
4351498 TTTG-TTTCTT-
1 TTTGCTTT-TTC
* *
4351508 TTTGCTATTTG
1 TTTGCTTTTTC
4351519 TTT--TTTTCTC
1 TTTGCTTTT-TC
4351529 TTTGCTCTTTTC
1 TTTGCT-TTTTC
4351541 T
1 T
4351542 CTTTGTTTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 26
0.71 0.04 0.25
Matches are distributed among these distances:
9 5 0.07
10 20 0.27
11 21 0.29
12 14 0.19
13 3 0.04
14 9 0.12
15 1 0.01
ACGTcount: A:0.03, C:0.17, G:0.10, T:0.71
Consensus pattern (11 bp):
TTTGCTTTTTC
Found at i:4351509 original size:14 final size:15
Alignment explanation
Indices: 4351492--4351549 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 15
4351482 TTTCCTTTGA
4351492 TTTT-TCTTTGTTTC
1 TTTTCTCTTTGTTTC
*
4351506 TTTTTGCTATTTGTTT-
1 -TTTT-CTCTTTGTTTC
*
4351522 TTTTCTCTTTG-CTC
1 TTTTCTCTTTGTTTC
4351536 TTTTCTCTTTGTTT
1 TTTTCTCTTTGTTT
4351550 TGATTTGATC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 1 0.03
14 17 0.49
15 9 0.26
17 8 0.23
ACGTcount: A:0.02, C:0.16, G:0.09, T:0.74
Consensus pattern (15 bp):
TTTTCTCTTTGTTTC
Found at i:4351509 original size:26 final size:26
Alignment explanation
Indices: 4351446--4351510 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
4351436 TCTTTTTGCT
*
4351446 TTTGTCTTCTTTTTCTTTGCTTTTTCG
1 TTTGT-TTCTTTTTCTTTGATTTTTCG
* *
4351473 TTTGCTAT-TTTTCCTTTGATTTTTC-
1 TTTG-TTTCTTTTTCTTTGATTTTTCG
4351498 TTTGTTTCTTTTT
1 TTTGTTTCTTTTT
4351511 GCTATTTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 2 0.06
25 8 0.26
26 15 0.48
27 5 0.16
28 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.09, T:0.72
Consensus pattern (26 bp):
TTTGTTTCTTTTTCTTTGATTTTTCG
Found at i:4352176 original size:20 final size:20
Alignment explanation
Indices: 4352138--4352176 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4352128 GGATAAATGC
*
4352138 AATGTTTCAATGTCACAAAG
1 AATGTTTCAAGGTCACAAAG
*
4352158 AATGTTTCAAGGTCTCAAA
1 AATGTTTCAAGGTCACAAA
4352177 AAGAGGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTTTCAAGGTCACAAAG
Found at i:4355348 original size:5 final size:5
Alignment explanation
Indices: 4355338--4355379 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
4355328 AAGATGAAGT
*
4355338 AAATA AAATA AAATA AAATA AAACA TAAAT- AAAT- AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA -AAATA AAATA AAATA AAA
4355380 CTCAACACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 8 0.24
5 22 0.67
6 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:4357120 original size:3 final size:3
Alignment explanation
Indices: 4357112--4357146 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4357102 TAAATTTCAA
4357112 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4357147 ATTAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4359510 original size:28 final size:29
Alignment explanation
Indices: 4359470--4359524 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
4359460 GTTAAAGTCT
4359470 GCAGTATTTTC-TTTTTTATTTTTATTCA
1 GCAGTATTTTCTTTTTTTATTTTTATTCA
*
4359498 GCAGTATTTTCTTTTTTTCTTTTTATT
1 GCAGTATTTTCTTTTTTTATTTTTATT
4359525 ATTGTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.15, C:0.11, G:0.07, T:0.67
Consensus pattern (29 bp):
GCAGTATTTTCTTTTTTTATTTTTATTCA
Found at i:4363978 original size:2 final size:2
Alignment explanation
Indices: 4363971--4364001 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4363961 AATTAAAAAT
*
4363971 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4364002 TTGTAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4364006 original size:12 final size:12
Alignment explanation
Indices: 4363971--4364006 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
4363961 AATTAAAAAT
*
4363971 TATATATATATA
1 TATATATATGTA
4363983 TATATATATGTA
1 TATATATATGTA
*
4363995 TATATATTTGTA
1 TATATATATGTA
4364007 AAAATATGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (12 bp):
TATATATATGTA
Found at i:4373826 original size:25 final size:25
Alignment explanation
Indices: 4373769--4373827 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 25
4373759 GGAGTTTTTT
4373769 TAAAATTTGAGAATTTTTTTTTAAA
1 TAAAATTTGAGAATTTTTTTTTAAA
*
4373794 TAATAATTTTA-AATTTTTATTTTAAA
1 TAA-AATTTGAGAATTTTT-TTTTAAA
4373820 TAAAATTT
1 TAAAATTT
4373828 AAAAAATTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (25 bp):
TAAAATTTGAGAATTTTTTTTTAAA
Found at i:4373954 original size:86 final size:86
Alignment explanation
Indices: 4373858--4374031 Score: 348
Period size: 86 Copynumber: 2.0 Consensus size: 86
4373848 TACGTGTCAT
4373858 TTGACGAAATCTTTTAACAATTGTTATAATCAAAATATTTCAACTAATAATGTTTATAGTGTTAA
1 TTGACGAAATCTTTTAACAATTGTTATAATCAAAATATTTCAACTAATAATGTTTATAGTGTTAA
4373923 ACACTTGATTGATAAAAAAAA
66 ACACTTGATTGATAAAAAAAA
4373944 TTGACGAAATCTTTTAACAATTGTTATAATCAAAATATTTCAACTAATAATGTTTATAGTGTTAA
1 TTGACGAAATCTTTTAACAATTGTTATAATCAAAATATTTCAACTAATAATGTTTATAGTGTTAA
4374009 ACACTTGATTGATAAAAAAAA
66 ACACTTGATTGATAAAAAAAA
4374030 TT
1 TT
4374032 AAAACACCTG
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (86 bp):
TTGACGAAATCTTTTAACAATTGTTATAATCAAAATATTTCAACTAATAATGTTTATAGTGTTAA
ACACTTGATTGATAAAAAAAA
Found at i:4383484 original size:10 final size:10
Alignment explanation
Indices: 4383469--4383496 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
4383459 TAGTAATCCT
4383469 TTAAAAGATG
1 TTAAAAGATG
4383479 TTAAAAGATG
1 TTAAAAGATG
4383489 TTAAAAGA
1 TTAAAAGA
4383497 CCTATAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.29
Consensus pattern (10 bp):
TTAAAAGATG
Found at i:4387745 original size:106 final size:103
Alignment explanation
Indices: 4387551--4387759 Score: 391
Period size: 106 Copynumber: 2.0 Consensus size: 103
4387541 ATAAGATGAG
4387551 GGAGTACATGAAGAATTAAAGAAAGGAAGTAAAATGAAATTTGGATAGAGTTCATAATAGAATTA
1 GGAGTACATGAAGAATTAAAGAAAGGAAGTAAAATGAAATTTGGATAGAGTTCATAATAGAATTA
4387616 GAAGTGAGATTTAACTTGTCATCAAGCTAATTAAAGAA
66 GAAGTGAGATTTAACTTGTCATCAAGCTAATTAAAGAA
4387654 GGAGTACATGAAGAATTAAAGAAAGGAAGTAGAAAATGAAATTTGGATAGAGTTCATAATAAGAA
1 GGAGTACATGAAGAATTAAAGAAAGGAAGT--AAAATGAAATTTGGATAGAGTTCATAAT-AGAA
4387719 TTAGAAGTGAGATTTAACTTGTCATCAAGCTAATTAAAGAA
63 TTAGAAGTGAGATTTAACTTGTCATCAAGCTAATTAAAGAA
4387760 TAGGAAAATT
Statistics
Matches: 103, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
103 30 0.29
105 28 0.27
106 45 0.44
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.26
Consensus pattern (103 bp):
GGAGTACATGAAGAATTAAAGAAAGGAAGTAAAATGAAATTTGGATAGAGTTCATAATAGAATTA
GAAGTGAGATTTAACTTGTCATCAAGCTAATTAAAGAA
Found at i:4387759 original size:41 final size:41
Alignment explanation
Indices: 4387714--4387842 Score: 102
Period size: 41 Copynumber: 3.3 Consensus size: 41
4387704 AGTTCATAAT
4387714 AAGAATTA-GAAGTGAGATTTAACTTGTCATCAAGCTAATTA
1 AAGAA-TAGGAAGTGAGATTTAACTTGTCATCAAGCTAATTA
* ***
4387755 AAGAATAGGAA---A-ATTTGGA-TTAGAGTTC-A--TAA-T-
1 AAGAATAGGAAGTGAGATTT-AACTT-GTCATCAAGCTAATTA
4387788 AAGAATTA-GAAGTGAGATTTAACTTGTCATCAAGCTAATTA
1 AAGAA-TAGGAAGTGAGATTTAACTTGTCATCAAGCTAATTA
4387829 AAGAATAGGAAGTG
1 AAGAATAGGAAGTG
4387843 TTAGAATTAG
Statistics
Matches: 65, Mismatches: 8, Indels: 30
0.63 0.08 0.29
Matches are distributed among these distances:
33 8 0.12
34 3 0.05
35 3 0.05
36 5 0.08
37 14 0.22
38 5 0.08
39 3 0.05
40 5 0.08
41 19 0.29
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.29
Consensus pattern (41 bp):
AAGAATAGGAAGTGAGATTTAACTTGTCATCAAGCTAATTA
Found at i:4387789 original size:74 final size:73
Alignment explanation
Indices: 4387692--4387839 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 73
4387682 GTAGAAAATG
4387692 AAATTTGGATAGAGTTCATAATAAGAATTAGAAGTGAGATTTAACTTGTCATCAAGCTAATTAAA
1 AAATTTGGATAGAGTTCATAATAAGAATTAGAAGTGAGATTTAACTTGTCATCAAGCTAATTAAA
4387757 GAATAGGA
66 GAATAGGA
4387765 AAATTTGGATTAGAGTTCATAATAAGAATTAGAAGTGAGATTTAACTTGTCATCAAGCTAATTAA
1 AAATTTGGA-TAGAGTTCATAATAAGAATTAGAAGTGAGATTTAACTTGTCATCAAGCTAATTAA
4387830 AGAATAGGA
65 AGAATAGGA
4387839 A
1 A
4387840 GTGTTAGAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 9 0.12
74 65 0.88
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (73 bp):
AAATTTGGATAGAGTTCATAATAAGAATTAGAAGTGAGATTTAACTTGTCATCAAGCTAATTAAA
GAATAGGA
Found at i:4388189 original size:64 final size:63
Alignment explanation
Indices: 4388114--4388234 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 63
4388104 ATTGTTCAAG
* * *
4388114 GTGTATCGATGCACATGAAGTGCATCGATGCACTACTTTAAAATAAAAACATCGAATACCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTT-AAATAAAAACATCGAATACCATCA
* * *
4388178 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTTAAATAAAAACATCGAATA
4388235 GGATTTATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
63 17 0.33
64 34 0.67
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTTAAATAAAAACATCGAATACCATCA
Found at i:4388262 original size:63 final size:64
Alignment explanation
Indices: 4388114--4388275 Score: 179
Period size: 63 Copynumber: 2.5 Consensus size: 64
4388104 ATTGTTCAAG
** *
4388114 GTGTATCGATGCACATGA-AGTGCATCGATGCACTACTTTAAAATAAAAACATCGAATACCATCA
1 GTGTATCGATGCACA-GATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACCATCA
* ** *
4388178 GTGTATCGATGCACA-AGTAGTGCATCGATGCACCCCCTT-AAATACAAACATCGAATAGGATTT
1 GTGTATCGATGCACAGA-TAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACCA-TC
4388241 A
64 A
* * *
4388242 -TGTATCGGTGCATAGATAGTGCATCGATTCACCC
1 GTGTATCGATGCACAGATAGTGCATCGATGCACCC
4388276 GTCAAGGGAT
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 47 0.56
64 36 0.43
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAGATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACCATCA
Found at i:4389590 original size:21 final size:21
Alignment explanation
Indices: 4389566--4389608 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4389556 AGATTACTAA
4389566 AGTCCTTGTATGGACTGAAGC
1 AGTCCTTGTATGGACTGAAGC
4389587 AGTCCTTGTATGGACTGAAGC
1 AGTCCTTGTATGGACTGAAGC
4389608 A
1 A
4389609 ATCTCCAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (21 bp):
AGTCCTTGTATGGACTGAAGC
Found at i:4395169 original size:55 final size:56
Alignment explanation
Indices: 4395100--4395217 Score: 229
Period size: 55 Copynumber: 2.1 Consensus size: 56
4395090 TGAATGTGAT
4395100 ATGTGAACATAAAAGATTAAGTGACATGAGCTAAGTGATCATATGAAAACAAG-AC
1 ATGTGAACATAAAAGATTAAGTGACATGAGCTAAGTGATCATATGAAAACAAGAAC
4395155 ATGTGAACATAAAAGATTAAGTGACATGAGCTAAGTGATCATATGAAAACAAGAAC
1 ATGTGAACATAAAAGATTAAGTGACATGAGCTAAGTGATCATATGAAAACAAGAAC
4395211 ATGTGAA
1 ATGTGAA
4395218 ATGAAGTATA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 53 0.85
56 9 0.15
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.22
Consensus pattern (56 bp):
ATGTGAACATAAAAGATTAAGTGACATGAGCTAAGTGATCATATGAAAACAAGAAC
Found at i:4395447 original size:20 final size:20
Alignment explanation
Indices: 4395395--4395452 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
4395385 GTTGAGGGTT
*
4395395 CATAGGTCTTTCGAGACATA
1 CATAGGTCATTCGAGACATA
* * * * *
4395415 CAGAGATCCTTCGGGATATA
1 CATAGGTCATTCGAGACATA
4395435 CATAGGTCATTCGAGACA
1 CATAGGTCATTCGAGACA
4395453 AATTTCACAT
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (20 bp):
CATAGGTCATTCGAGACATA
Found at i:4397049 original size:19 final size:19
Alignment explanation
Indices: 4397025--4397071 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
4397015 CAGGAGGCGG
4397025 AACCCAAATAAACCGAGAT
1 AACCCAAATAAACCGAGAT
4397044 AACCCAAATAAACCGAGAT
1 AACCCAAATAAACCGAGAT
4397063 AACCCAAAT
1 AACCCAAAT
4397072 CTTTTATGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.53, C:0.28, G:0.09, T:0.11
Consensus pattern (19 bp):
AACCCAAATAAACCGAGAT
Found at i:4404442 original size:121 final size:121
Alignment explanation
Indices: 4404228--4404471 Score: 479
Period size: 121 Copynumber: 2.0 Consensus size: 121
4404218 CCCTCAGCTA
*
4404228 TAAATAATACGCTCTTAACCCGTAAACATCACCCAACAATCCTCTTATCTTTGATTCAGAAGTTT
1 TAAATAATACGCTCTCAACCCGTAAACATCACCCAACAATCCTCTTATCTTTGATTCAGAAGTTT
4404293 GTTTGATCTTTCGTTGTAAGGTATTTTTTTAATATATAATATTTTTTATATATGAT
66 GTTTGATCTTTCGTTGTAAGGTATTTTTTTAATATATAATATTTTTTATATATGAT
4404349 TAAATAATACGCTCTCAACCCGTAAACATCACCCAACAATCCTCTTATCTTTGATTCAGAAGTTT
1 TAAATAATACGCTCTCAACCCGTAAACATCACCCAACAATCCTCTTATCTTTGATTCAGAAGTTT
4404414 GTTTGATCTTTCGTTGTAAGGTATTTTTTTAATATATAATATTTTTTATATATGAT
66 GTTTGATCTTTCGTTGTAAGGTATTTTTTTAATATATAATATTTTTTATATATGAT
4404470 TA
1 TA
4404472 TTTGAAAAAA
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (121 bp):
TAAATAATACGCTCTCAACCCGTAAACATCACCCAACAATCCTCTTATCTTTGATTCAGAAGTTT
GTTTGATCTTTCGTTGTAAGGTATTTTTTTAATATATAATATTTTTTATATATGAT
Found at i:4404528 original size:14 final size:14
Alignment explanation
Indices: 4404509--4404535 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4404499 AATTCATATT
4404509 TTATTTAAATTATA
1 TTATTTAAATTATA
4404523 TTATTTAAATTAT
1 TTATTTAAATTAT
4404536 TTACGTTTAT
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:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTAAATTATA
Found at i:4407687 original size:13 final size:13
Alignment explanation
Indices: 4407669--4407694 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4407659 GATTAATTAA
4407669 ACAAGAAAACGAT
1 ACAAGAAAACGAT
4407682 ACAAGAAAACGAT
1 ACAAGAAAACGAT
4407695 GAAGAAGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.08
Consensus pattern (13 bp):
ACAAGAAAACGAT
Found at i:4408746 original size:23 final size:23
Alignment explanation
Indices: 4408716--4408762 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4408706 AAACATAGAA
4408716 CCATAATATCCACCAAGAGGGGT
1 CCATAATATCCACCAAGAGGGGT
4408739 CCATAATATCCACCAAGAGGGGT
1 CCATAATATCCACCAAGAGGGGT
4408762 C
1 C
4408763 ATATAACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (23 bp):
CCATAATATCCACCAAGAGGGGT
Found at i:4410392 original size:30 final size:31
Alignment explanation
Indices: 4410357--4410427 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 31
4410347 CGCTCTCCTA
* *
4410357 AAATTATTAATAATTACAAAATT-AATATAT
1 AAATTATTAATAATTAAAAAATTAAATAAAT
4410387 -AA--ATTAATAA-TAAAAAATTAAATAAAT
1 AAATTATTAATAATTAAAAAATTAAATAAAT
*
4410414 AAATTATTACTAAT
1 AAATTATTAATAAT
4410428 AATTTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
26 8 0.24
27 14 0.42
28 2 0.06
29 2 0.06
30 7 0.21
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (31 bp):
AAATTATTAATAATTAAAAAATTAAATAAAT
Found at i:4410436 original size:27 final size:27
Alignment explanation
Indices: 4410362--4410419 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
4410352 TCCTAAAATT
* *
4410362 ATTAATAATTACAAAATT-AATATATAA
1 ATTAATAA-TAAAAAATTAAATAAATAA
4410389 ATTAATAATAAAAAATTAAATAAATAA
1 ATTAATAATAAAAAATTAAATAAATAA
4410416 ATTA
1 ATTA
4410420 TTACTAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
ATTAATAATAAAAAATTAAATAAATAA
Found at i:4413800 original size:28 final size:28
Alignment explanation
Indices: 4413745--4413805 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
4413735 TCGAAATGAA
* * *
4413745 ATAAAATTAAAAGTTTAATGATTTAAAT
1 ATAAAATTAAAAGTTTAATAACTAAAAT
* * *
4413773 GTAAATTTAAAAGTTTGATAACTAAAAT
1 ATAAAATTAAAAGTTTAATAACTAAAAT
4413801 ATAAA
1 ATAAA
4413806 CATTCTAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (28 bp):
ATAAAATTAAAAGTTTAATAACTAAAAT
Found at i:4414498 original size:9 final size:9
Alignment explanation
Indices: 4414486--4414518 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
4414476 TTAATATTTG
4414486 TATTTAATT
1 TATTTAATT
*
4414495 TATTTAA-G
1 TATTTAATT
4414503 TATTTAATT
1 TATTTAATT
4414512 TATTTAA
1 TATTTAA
4414519 CTAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (9 bp):
TATTTAATT
Found at i:4414507 original size:17 final size:17
Alignment explanation
Indices: 4414485--4414518 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4414475 TTTAATATTT
4414485 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
4414502 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
4414519 CTAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:4416324 original size:33 final size:33
Alignment explanation
Indices: 4416264--4416331 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
4416254 CCCGATGCCA
*** * *
4416264 CCGCCGCCACCATCACCTGGTTTTATGACCCCT
1 CCGCCGCCACCATCACAAAGTTATATGACCACT
*
4416297 CCGCCGCCACCTTCACAAAGTTATATGACCACT
1 CCGCCGCCACCATCACAAAGTTATATGACCACT
4416330 CC
1 CC
4416332 TGGAGACTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.21, C:0.44, G:0.13, T:0.22
Consensus pattern (33 bp):
CCGCCGCCACCATCACAAAGTTATATGACCACT
Found at i:4423412 original size:19 final size:19
Alignment explanation
Indices: 4423385--4423421 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4423375 CTCCAACAAG
*
4423385 GGAAGTGAATTCTATCATT
1 GGAAGTGAATTCCATCATT
*
4423404 GGAATTGAATTCCATCAT
1 GGAAGTGAATTCCATCAT
4423422 AGAATGGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (19 bp):
GGAAGTGAATTCCATCATT
Found at i:4438983 original size:26 final size:27
Alignment explanation
Indices: 4438954--4439037 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
4438944 ATTTCCTCTA
4438954 CCATTATCAACAAAACCT-G-ATGC-ACT
1 CCATTATCAACAAAA-CTGGCA-GCAACT
*
4438980 CCATTCTCAACAAAACTGGCAGCAACT
1 CCATTATCAACAAAACTGGCAGCAACT
* *
4439007 CCATTTTCAACAAAAAC-GGTAGCAACT
1 CCATTATCAAC-AAAACTGGCAGCAACT
4439034 CCAT
1 CCAT
4439038 GGTCAATCCA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.04
26 17 0.33
27 27 0.53
28 5 0.10
ACGTcount: A:0.38, C:0.31, G:0.10, T:0.21
Consensus pattern (27 bp):
CCATTATCAACAAAACTGGCAGCAACT
Found at i:4439043 original size:27 final size:27
Alignment explanation
Indices: 4438977--4439037 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
4438967 AACCTGATGC
4438977 ACTCCATTCTCAACAAAACTGGCAGCA
1 ACTCCATTCTCAACAAAACTGGCAGCA
* *
4439004 ACTCCATTTTCAACAAAAAC-GGTAGCA
1 ACTCCATTCTCAAC-AAAACTGGCAGCA
4439031 ACTCCAT
1 ACTCCAT
4439038 GGTCAATCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.38, C:0.31, G:0.10, T:0.21
Consensus pattern (27 bp):
ACTCCATTCTCAACAAAACTGGCAGCA
Found at i:4459862 original size:3 final size:3
Alignment explanation
Indices: 4459854--4459910 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
4459844 TTATTTTAAA
**
4459854 ATT ATT ATT AAC ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4459901 ATT ATT ATT A
1 ATT ATT ATT A
4459911 AATAATAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:4459871 original size:20 final size:20
Alignment explanation
Indices: 4459846--4459883 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4459836 TTTCCATTTT
4459846 ATTTTAAAATTATTATTAAC
1 ATTTTAAAATTATTATTAAC
**
4459866 ATTTTATTATTATTATTA
1 ATTTTAAAATTATTATTA
4459884 TTATTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTAAAATTATTATTAAC
Found at i:4460007 original size:29 final size:29
Alignment explanation
Indices: 4459960--4460029 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
4459950 TACTAAACCG
*
4459960 AAGCCCAGATAGTAGACCCGACCCGGTCC
1 AAGCCCAGATAGCAGACCCGACCCGGTCC
* *
4459989 AAGCCCAGATAGCATACCCGACCTGGTCC
1 AAGCCCAGATAGCAGACCCGACCCGGTCC
4460018 AAGCCCAGATAG
1 AAGCCCAGATAG
4460030 TAGATCCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.30, C:0.36, G:0.23, T:0.11
Consensus pattern (29 bp):
AAGCCCAGATAGCAGACCCGACCCGGTCC
Found at i:4462201 original size:63 final size:62
Alignment explanation
Indices: 4462068--4462222 Score: 244
Period size: 63 Copynumber: 2.5 Consensus size: 62
4462058 CACTCACCAT
4462068 ATCGAATGCATTTTATGCATCGATGCACTACCATGCATCGATGCACTAAGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACTACCATGCATCGATGCACTAAGTTTTATGAAAAC
*
4462130 ATCGAATGCATTTTATGCATCGATGCACATACCATGC-TCGATGCACTCATGCTTGTT-TG-AAA
1 ATCGAATGCATTTTATGCATCGATGCAC-TACCATGCATCGATGCACT-AAG-TT-TTATGAAAA
4462192 C
62 C
4462193 ATCGAATGCATTTTATGCATCGATGCACTA
1 ATCGAATGCATTTTATGCATCGATGCACTA
4462223 AGGGTCCAAC
Statistics
Matches: 88, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
62 40 0.45
63 42 0.48
64 4 0.05
65 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (62 bp):
ATCGAATGCATTTTATGCATCGATGCACTACCATGCATCGATGCACTAAGTTTTATGAAAAC
Found at i:4462812 original size:19 final size:19
Alignment explanation
Indices: 4462788--4462824 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4462778 AGTGGACGTA
4462788 GACTTTGGTTGAGAAAGTC
1 GACTTTGGTTGAGAAAGTC
4462807 GACTTTGGTTGAGAAAGT
1 GACTTTGGTTGAGAAAGT
4462825 TAAACCACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.08, G:0.32, T:0.32
Consensus pattern (19 bp):
GACTTTGGTTGAGAAAGTC
Found at i:4464224 original size:36 final size:36
Alignment explanation
Indices: 4464176--4464244 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
4464166 CTATGCACAT
*
4464176 AAAGATCATGTTATATTGATACCAAAAGTATTCCAC
1 AAAGATCATGTTAGATTGATACCAAAAGTATTCCAC
*
4464212 AAAGATCTTGTTAGATTGATACCAAAAGTATTC
1 AAAGATCATGTTAGATTGATACCAAAAGTATTC
4464245 TACGGTAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (36 bp):
AAAGATCATGTTAGATTGATACCAAAAGTATTCCAC
Found at i:4467396 original size:7 final size:7
Alignment explanation
Indices: 4467384--4467466 Score: 98
Period size: 7 Copynumber: 11.9 Consensus size: 7
4467374 ACTCATTCAT
4467384 AAGAAAA
1 AAGAAAA
4467391 AAGAAAA
1 AAGAAAA
*
4467398 AAGGAAA
1 AAGAAAA
4467405 AAGAAAA
1 AAGAAAA
4467412 AAGAAAA
1 AAGAAAA
4467419 AAGGAAAA
1 AA-GAAAA
*
4467427 AGGAAAA
1 AAGAAAA
*
4467434 ATG-AAA
1 AAGAAAA
4467440 AAGAAAA
1 AAGAAAA
*
4467447 AAGGAAAG
1 AA-GAAAA
4467455 AA-AAAA
1 AAGAAAA
4467461 AAGAAA
1 AAGAAA
4467467 TTGAATCAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
6 10 0.15
7 43 0.66
8 12 0.18
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (7 bp):
AAGAAAA
Found at i:4467410 original size:21 final size:22
Alignment explanation
Indices: 4467386--4467463 Score: 108
Period size: 21 Copynumber: 3.7 Consensus size: 22
4467376 TCATTCATAA
4467386 GAAAAAAGAAAAAAGGAAAAA-
1 GAAAAAAGAAAAAAGGAAAAAG
4467407 GAAAAAAGAAAAAAGGAAAAAG
1 GAAAAAAGAAAAAAGGAAAAAG
* *
4467429 GAAAAATG-AAAAAGAAAAAAG
1 GAAAAAAGAAAAAAGGAAAAAG
*
4467450 GAAAGAA-AAAAAAG
1 GAAAAAAGAAAAAAG
4467464 AAATTGAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 44 0.86
22 7 0.14
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (22 bp):
GAAAAAAGAAAAAAGGAAAAAG
Found at i:4469115 original size:54 final size:54
Alignment explanation
Indices: 4469041--4469157 Score: 162
Period size: 54 Copynumber: 2.1 Consensus size: 54
4469031 AGAACTTCAC
* * * * *
4469041 TTACGAGAAATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATTTT
1 TTACGA-ACATCTGGGCAGAAACCACAAGAAAGGATGAATGTATTGTCAAATGTT
* *
4469096 TTACGAACATCTGTGCAGAAACTACAAGAAAGGATGAATGTATTGTCAAATGTT
1 TTACGAACATCTGGGCAGAAACCACAAGAAAGGATGAATGTATTGTCAAATGTT
4469150 TTACGAAC
1 TTACGAAC
4469158 CAGTGATTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
54 49 0.89
55 6 0.11
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (54 bp):
TTACGAACATCTGGGCAGAAACCACAAGAAAGGATGAATGTATTGTCAAATGTT
Found at i:4470617 original size:217 final size:218
Alignment explanation
Indices: 4470230--4470847 Score: 979
Period size: 218 Copynumber: 2.8 Consensus size: 218
4470220 AACTATTTCC
* *
4470230 CTAGATTATAAAGCCTTCAGGTCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTT
1 CTAGATGATAAAGCCTTCAGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTT
*
4470295 TAGAAACTAAGCCTTCAGGGGTTTCCTAATTATCTCAAGAGAGCTGTTAAAGGAAGCTAAGCCTA
66 TAGAAACTAAGCCTTCAGGGGTTTCCTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTA
* * * *
4470360 ACAAAGGGGTTACTTGACAACTAAGAAATTAAGTCTTCGGGGGTTTCTT-ATTTTTAAATCCTTC
131 ACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAATCCTTC
* *
4470424 AGGTCAT-TGGTAAGCCTTTTGTG
196 AGGTCATCT-GTAAGCCTTTCGAG
*
4470447 CTAGATGATAAAGCCTTCAGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTTAAATGAGATTT
1 CTAGATGATAAAGCCTTCAGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTT
* * *
4470512 TAGAAACTAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCTA
66 TAGAAACTAAGCCTTCAGGGGTTTCCTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTA
* * *
4470577 ACAAAGAGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTT
131 ACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAATCCTTC
* *
4470642 GGGTCATCTGTAATCCTTTCGAG
196 AGGTCATCTGTAAGCCTTTCGAG
* * * **
4470665 CAACATGATAAAGCCTTCAGGTCATCCATAAGATCTTCAGTGCAGGATGTTGGCAAATGAGATTT
1 CTAGATGATAAAGCCTTCAGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTT
* *
4470730 TAGAAACTAAGCCTTCAGGGATTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTA
66 TAGAAACTAAGCCTTCAGGGGTTTCCTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTA
*
4470795 ACAAAGGGGTTCCTTGACAATTAAGAAACTAAGCCTTCGGGGGTTTCTTGATT
131 ACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATT
4470848 CATAAAACTT
Statistics
Matches: 368, Mismatches: 31, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
217 168 0.46
218 199 0.54
219 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (218 bp):
CTAGATGATAAAGCCTTCAGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTT
TAGAAACTAAGCCTTCAGGGGTTTCCTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTA
ACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAATCCTTC
AGGTCATCTGTAAGCCTTTCGAG
Found at i:4472636 original size:15 final size:16
Alignment explanation
Indices: 4472616--4472647 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
4472606 TAAAATACTA
4472616 TATTTAATTTAT-TTT
1 TATTTAATTTATATTT
4472631 TATTTAATTTATATTT
1 TATTTAATTTATATTT
4472647 T
1 T
4472648 TTACGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTTAATTTATATTT
Found at i:4472690 original size:17 final size:17
Alignment explanation
Indices: 4472660--4472698 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4472650 ACGAAAAAAT
4472660 TATTATATTTTTTTAAA
1 TATTATATTTTTTTAAA
*
4472677 TATT-TATTTATTTTTAA
1 TATTATATTT-TTTTAAA
4472694 TATTA
1 TATTA
4472699 AAGAAATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTATATTTTTTTAAA
Found at i:4472794 original size:150 final size:148
Alignment explanation
Indices: 4472529--4472800 Score: 342
Period size: 150 Copynumber: 1.8 Consensus size: 148
4472519 TAATAGTATT
** *
4472529 TATTTATTTATTTTAATATTAAGAAAGGTGTTGTCTTAAAGTAACTAGATGCTATTTTTCTGATA
1 TATTTATTTATTTTAATATTAAGAAAGGTAATGTCTTAAAGCAACTAGATGCTATTTTTCTGATA
** * *
4472594 TTTTTAAATAAATAAAATACTATATTTAATTTATTTTTATTTAATTTATAT-TTTTTACGAAAAA
66 TTTTTAAATAAATAAAATACTATATTTAATTTATAATCATTT-ATATATATGTTTTTACGAAAAA
4472658 ATTATTATATTTTTTTAAA
130 ATTATTATATTTTTTTAAA
4472677 TATTTATTTATTTTTAATATTAAAGAAATGG-AATGTCTTAAAGCAACTAGATGAC-A-TTTTCT
1 TATTTATTTA-TTTTAATATT-AAGAAA-GGTAATGTCTTAAAGCAACTAGATG-CTATTTTTCT
4472739 GATATTTTTAAATAAAT-AAATACCT-TATTTATAATTTATAAAATCATTT-TATATATGTTTTT
62 GATATTTTTAAATAAATAAAATA-CTATA-TT-TAATTTAT--AATCATTTATATATATGTTTTT
4472801 TTCTTAGAAT
Statistics
Matches: 107, Mismatches: 7, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
148 17 0.16
149 37 0.35
150 40 0.37
151 8 0.07
152 5 0.05
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (148 bp):
TATTTATTTATTTTAATATTAAGAAAGGTAATGTCTTAAAGCAACTAGATGCTATTTTTCTGATA
TTTTTAAATAAATAAAATACTATATTTAATTTATAATCATTTATATATATGTTTTTACGAAAAAA
TTATTATATTTTTTTAAA
Found at i:4474641 original size:19 final size:19
Alignment explanation
Indices: 4474617--4474663 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
4474607 ATGAAAACTC
4474617 TCTTCTTCTTCATTTGCTT
1 TCTTCTTCTTCATTTGCTT
4474636 TCTTCTTCTTCATTTGCTT
1 TCTTCTTCTTCATTTGCTT
4474655 TCTTCTTCT
1 TCTTCTTCT
4474664 CCAACGTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.04, C:0.28, G:0.04, T:0.64
Consensus pattern (19 bp):
TCTTCTTCTTCATTTGCTT
Found at i:4476729 original size:22 final size:22
Alignment explanation
Indices: 4476690--4476732 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4476680 GCACTGTAGC
*
4476690 ACTGTTCATGGCACTGTTCATT
1 ACTGTTCACGGCACTGTTCATT
* *
4476712 ACTGTTCACGGTATTGTTCAT
1 ACTGTTCACGGCACTGTTCAT
4476733 ACTATATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (22 bp):
ACTGTTCACGGCACTGTTCATT
Found at i:4478850 original size:20 final size:20
Alignment explanation
Indices: 4478820--4478991 Score: 98
Period size: 20 Copynumber: 8.4 Consensus size: 20
4478810 GTTTCCAGAT
*
4478820 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
4478840 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
** *
4478860 TTCGCGTTGCGATTTTCCGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
4478883 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* *
4478903 TCGCAATGCGAGTATGACTA
1 TCGCAATGCGATTCTGACTA
* * * *
4478923 TCGCAACGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
4478943 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
4478963 TCGCAACGCGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
4478983 TCGCAATGC
1 TCGCAATGC
4478992 TATTTTCAAA
Statistics
Matches: 115, Mismatches: 28, Indels: 18
0.71 0.17 0.11
Matches are distributed among these distances:
19 4 0.03
20 86 0.75
21 12 0.10
22 9 0.08
23 3 0.03
24 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:4478892 original size:22 final size:22
Alignment explanation
Indices: 4478835--4478893 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
4478825 ACGCGATTCT
4478835 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
4478857 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
4478878 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
4478894 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:4478991 original size:40 final size:40
Alignment explanation
Indices: 4478878--4478973 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
4478868 GCGATTTTCC
*
4478878 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATGCGAGTAT
* *
4478918 GACTATCGCAACGCGAATATGTAAATCGCAATGCGATTCT
1 GACTATCGCAACGCGAATATGTAAATCGCAATGCGAGTAT
4478958 GACTATCGCAACGCGA
1 GACTATCGCAACGCGA
4478974 TTCTGACTGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (40 bp):
GACTATCGCAACGCGAATATGTAAATCGCAATGCGAGTAT
Found at i:4479283 original size:9 final size:9
Alignment explanation
Indices: 4479269--4479296 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4479259 CAGAAATGAA
4479269 AAATCAACC
1 AAATCAACC
4479278 AAATCAACC
1 AAATCAACC
4479287 AAATCAACC
1 AAATCAACC
4479296 A
1 A
4479297 CCGAGGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.32, G:0.00, T:0.11
Consensus pattern (9 bp):
AAATCAACC
Found at i:4479630 original size:19 final size:19
Alignment explanation
Indices: 4479608--4479714 Score: 81
Period size: 20 Copynumber: 5.5 Consensus size: 19
4479598 AGAATCGCAA
4479608 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCA-TTTCGCGT
4479627 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
** * *
4479646 TGCGATAGTCAAATTCGCGA
1 TGCGATTTTC-ATTTCGCGT
* ** *
4479666 TGGGATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
* *
4479686 TGCAATTTTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
4479706 TGCGATTTT
1 TGCGATTTT
4479715 AAGTTTCAGA
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
19 26 0.36
20 46 0.64
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:4479721 original size:20 final size:20
Alignment explanation
Indices: 4479678--4479721 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4479668 GGATAGTCAT
* *
4479678 TTTCGTGTTGCAATTTTCAT
1 TTTCGTGTTGCAATTTTAAG
*
4479698 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCAATTTTAAG
4479718 TTTC
1 TTTC
4479722 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCAATTTTAAG
Found at i:4481472 original size:18 final size:18
Alignment explanation
Indices: 4481449--4481498 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
4481439 TTTACTCGTA
4481449 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
4481467 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
4481485 ATTTCACTTAGATT
1 ATTTCACTTAGATT
4481499 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:4481671 original size:20 final size:20
Alignment explanation
Indices: 4481646--4481691 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
4481636 TAGTTTACTT
*
4481646 TCGCAACGCGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* **
4481666 TCGCAACATGAATTTGACTA
1 TCGCAACACGAAAATGACTA
4481686 TCGCAA
1 TCGCAA
4481692 TGAAGAATCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:4481794 original size:18 final size:18
Alignment explanation
Indices: 4481736--4481801 Score: 87
Period size: 20 Copynumber: 3.4 Consensus size: 18
4481726 CGATTCTCTC
*
4481736 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTC--ATTCGT
4481756 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCA--TTCGT
4481776 GTTGCGATAGTCATTCGT
1 GTTGCGATAGTCATTCGT
4481794 GTTGCGAT
1 GTTGCGAT
4481802 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
18 14 0.33
20 29 0.67
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (18 bp):
GTTGCGATAGTCATTCGT
Found at i:4482310 original size:42 final size:42
Alignment explanation
Indices: 4482247--4482329 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
4482237 CACCAGTCAT
*
4482247 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* * * *
4482289 CGTTCAAGAGGCTACTGTCATCGCTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
4482330 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:4483763 original size:36 final size:30
Alignment explanation
Indices: 4483683--4483748 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
4483673 ATAAGAGTTG
4483683 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
4483713 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
4483743 ATTTGT
1 ATTTGT
4483749 GCTTGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:4483869 original size:20 final size:20
Alignment explanation
Indices: 4483844--4484048 Score: 164
Period size: 20 Copynumber: 10.8 Consensus size: 20
4483834 GCGATTTTCT
*
4483844 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
4483864 CGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * *
4483884 CGTTGTGATAGTTAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
4483904 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* **
4483924 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
4483944 CATTGCGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
*
4483958 CGTTGCTATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
4483978 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
4483998 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
4484012 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
4484032 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
4484049 GAATGTGTAA
Statistics
Matches: 145, Mismatches: 28, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
14 19 0.13
16 2 0.01
18 2 0.01
19 2 0.01
20 120 0.83
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:4483875 original size:54 final size:54
Alignment explanation
Indices: 4483805--4484045 Score: 250
Period size: 54 Copynumber: 4.4 Consensus size: 54
4483795 TCTGCATCAT
* * * *
4483805 ATTCGCGTTGCGATAGTC-TAATACACTTTGCGATTTTCTCGTTGCGATAGTCAA
1 ATTCGCGTTGCGATAGTCAT-ATTCGCATTGCGATTATCTCGTTGCGATAGTCAA
* * * * * * *
4483859 ATTCCCGTTGCAATAGTCAAATTCGCGTTGTGATAGTTAAATTTGCGTTGCGATAGTCAT
1 ATTCGCGTTGCGATAGTCATATTCGCATTGCG--A-TT--ATCT-CGTTGCGATAGTCAA
* * *
4483919 ATTCGCGTTGCAATAGTCATTTTCGCATTGCGATTATCTCGTTGCTATAGTCAA
1 ATTCGCGTTGCGATAGTCATATTCGCATTGCGATTATCTCGTTGCGATAGTCAA
* * *
4483973 ATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATATTCAA
1 ATTCGCGTTGCGATAGTCATATTCGCATTGCGATTATCTCGTTGCGATAGTCAA
*
4484027 ATTCACGTTGCGATAGTCA
1 ATTCGCGTTGCGATAGTCA
4484046 AATGAATGTG
Statistics
Matches: 157, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
54 105 0.67
55 3 0.02
56 1 0.01
57 4 0.03
58 1 0.01
59 2 0.01
60 41 0.26
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (54 bp):
ATTCGCGTTGCGATAGTCATATTCGCATTGCGATTATCTCGTTGCGATAGTCAA
Found at i:4484246 original size:18 final size:18
Alignment explanation
Indices: 4484223--4484257 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4484213 AAGCCGGTTG
4484223 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
4484241 TGATTGCGATTTTGATT
1 TGATTGAGATTTTGATT
4484258 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:4487445 original size:20 final size:20
Alignment explanation
Indices: 4487378--4487511 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
4487368 TTGAAATTCA
* * *
4487378 GCATTGCGACAGTCAGAACC
1 GCATTGCGATAGTCATAATC
* * *
4487398 GCGTTGCAATAGTCAGAATC
1 GCATTGCGATAGTCATAATC
4487418 GCATTGCGATAGTCATAATC
1 GCATTGCGATAGTCATAATC
* *
4487438 GCATTGCGAT-TTACATATTC
1 GCATTGCGATAGT-CATAATC
* *
4487458 GCGTTGCGATAGTCATACTC
1 GCATTGCGATAGTCATAATC
* *
4487478 GCATTGCGAT-TTACATATTC
1 GCATTGCGATAGT-CATAATC
4487498 GCATTGCGATAGTC
1 GCATTGCGATAGTC
4487512 GGAAAATTGC
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
19 2 0.02
20 90 0.96
21 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (20 bp):
GCATTGCGATAGTCATAATC
Found at i:4487465 original size:40 final size:40
Alignment explanation
Indices: 4487416--4487511 Score: 174
Period size: 40 Copynumber: 2.4 Consensus size: 40
4487406 ATAGTCAGAA
4487416 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
* *
4487456 TCGCGTTGCGATAGTCATACTCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
4487496 TCGCATTGCGATAGTC
1 TCGCATTGCGATAGTC
4487512 GGAAAATTGC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
Found at i:4489238 original size:27 final size:26
Alignment explanation
Indices: 4489206--4489257 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4489196 TACCGGATTC
4489206 ATCAATTGACTTTCATATTAATATTTT
1 ATCAATTGA-TTTCATATTAATATTTT
* **
4489233 ATCAATTTATTTTGTATTAATATTT
1 ATCAATTGATTTCATATTAATATTT
4489258 CATCTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.56
Consensus pattern (26 bp):
ATCAATTGATTTCATATTAATATTTT
Found at i:4497630 original size:19 final size:18
Alignment explanation
Indices: 4497606--4497645 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
4497596 ATTTTATTCA
4497606 TATCATGAATAATATTATT
1 TATCATGAATAATATT-TT
* *
4497625 TATCATGTATTATATTTT
1 TATCATGAATAATATTTT
4497643 TAT
1 TAT
4497646 TTTTATTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (18 bp):
TATCATGAATAATATTTT
Found at i:4502528 original size:29 final size:30
Alignment explanation
Indices: 4502462--4502543 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
4502452 TAGTCATAAA
* *
4502462 TTCATGTTTATGCTATTTTAGTCCTTTAACT
1 TTCATGTTT-TGCTATTTTAGTCCTGTAACG
4502493 TTC-TGTTTTGCTATTTTAG-CCATGTAA-G
1 TTCATGTTTTGCTATTTTAGTCC-TGTAACG
*
4502521 TTCATGTTTT-ATCATTTTAGTCC
1 TTCATGTTTTGCT-ATTTTAGTCC
4502544 CCGAAATTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 6 0.14
29 28 0.64
30 7 0.16
31 3 0.07
ACGTcount: A:0.18, C:0.16, G:0.12, T:0.54
Consensus pattern (30 bp):
TTCATGTTTTGCTATTTTAGTCCTGTAACG
Found at i:4506871 original size:105 final size:106
Alignment explanation
Indices: 4506688--4506903 Score: 319
Period size: 105 Copynumber: 2.0 Consensus size: 106
4506678 CATCACTAAT
* * ** *
4506688 ATAATAGTGTCGAACATTTGGTCACTAAAAAAACACTTGGTGTGACAACATTGGTGGTCACAAAA
1 ATAATAGTATCAAACATTTGGTCACTAAAAAAACACTTGGTGTGACAACATTAATGCTCACAAAA
* *
4506753 TATATTTTTAGTGTCAAACAAATTTATCACAATTTCTATGG
66 TATATTTTTAGTGTCAAACAAATTCATCACAATTTATATGG
* *
4506794 ATAATAGTATCAAACATTTGGTCACT-AAAAAATACTTGGTGTGACAATATTAATGACT-ACAAA
1 ATAATAGTATCAAACATTTGGTCACTAAAAAAACACTTGGTGTGACAACATTAATG-CTCACAAA
*
4506857 ATATATTTTTAGTGTCAAACAAATTCATCACAATTTATATTG
65 ATATATTTTTAGTGTCAAACAAATTCATCACAATTTATATGG
4506899 ATAAT
1 ATAAT
4506904 TGTGTCGAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
105 74 0.75
106 25 0.25
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (106 bp):
ATAATAGTATCAAACATTTGGTCACTAAAAAAACACTTGGTGTGACAACATTAATGCTCACAAAA
TATATTTTTAGTGTCAAACAAATTCATCACAATTTATATGG
Found at i:4508026 original size:31 final size:31
Alignment explanation
Indices: 4507981--4508040 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
4507971 TTATAAGGGT
* * *
4507981 AGTTTCATGATAACAATTATTGGAAAAAAATG
1 AGTTTCATAATAACAAATATT-AAAAAAAATG
4508013 AGTTTC-TAATAACAAATATTAAAAAAAA
1 AGTTTCATAATAACAAATATTAAAAAAAA
4508041 GTAAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.28
31 12 0.48
32 6 0.24
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (31 bp):
AGTTTCATAATAACAAATATTAAAAAAAATG
Found at i:4508887 original size:24 final size:24
Alignment explanation
Indices: 4508860--4508945 Score: 84
Period size: 24 Copynumber: 3.6 Consensus size: 24
4508850 TATATCAAAA
*
4508860 ATCAAAACATAAAT-CAAGTCAAGT
1 ATCAAATCA-AAATCCAAGTCAAGT
* * *
4508884 ATCATATCAAACTCCAGGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
4508908 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
4508932 ATCATATCAGAATC
1 ATCAAATCAAAATC
4508946 TATGTCAGAT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 3 0.06
24 49 0.94
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23
Consensus pattern (24 bp):
ATCAAATCAAAATCCAAGTCAAGT
Done.