Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 49
Found at i:2195158 original size:21 final size:21
Alignment explanation
Indices: 2195104--2195159 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
2195094 AACAACTATG
*
2195104 GAAGGGTGAAGGGGGAATAGA
1 GAAGGGAGAAGGGGGAATAGA
* *
2195125 TAAGGGGGAAGGGGGAATAGA
1 GAAGGGAGAAGGGGGAATAGA
2195146 GAA-GGAGAGAGGGG
1 GAAGGGAGA-AGGGG
2195160 ACAGAACACG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.38, C:0.00, G:0.55, T:0.07
Consensus pattern (21 bp):
GAAGGGAGAAGGGGGAATAGA
Found at i:2197753 original size:3 final size:3
Alignment explanation
Indices: 2197745--2197832 Score: 137
Period size: 3 Copynumber: 29.7 Consensus size: 3
2197735 TTAATATATT
2197745 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
2197789 TAA T-A TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2197833 TGGATAAAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.08
3 68 0.85
4 6 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2198168 original size:119 final size:116
Alignment explanation
Indices: 2197987--2198865 Score: 1416
Period size: 119 Copynumber: 7.5 Consensus size: 116
2197977 TTCTCCAGAT
** * *
2197987 GAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGTTCCATCAAATGATGAATTCAAGCAAA
1 GAGTTCTTCTCATTATGAACTTTCT-CTGGAAATGATGATCCATCAATTGATGAATTCAAGCAAA
*
2198052 AGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
2198104 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAA--CTTTCTCTGGAAATGATGATCCATCAA-TTGATGAATTCAAGCA
2198169 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
63 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
2198223 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACT-TT-CTCTGGAAATGATGATCCATCAA-TTGATGAATTCAAGCA
*
2198288 AAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---
63 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
2198339 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAA
1 GAGTTCTTCTCATTATGAACTTTCTCTGGAAATG-ATGATCCATCAATTGATGAATTCAAGCAAA
*
2198404 AGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---
65 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
2198453 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAA
1 GAGTTCTTCTCATTATGAACTTTCTCTGGAAATG-ATGATCCATCAATTGATGAATTCAAGCAAA
*
2198518 AGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---
65 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
2198567 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAA
1 GAGTTCTTCTCATTATGAACTTTCTCTGGAAATG-ATGATCCATCAATTGATGAATTCAAGCAAA
2198632 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
2198684 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACT-TT-CTCTGGAAATGATGATCCATC-AATTGATGAATTCAAGCA
2198749 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
63 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
2198803 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAGTTTGATGAATTCAAG
1 GAGTTCTTCTCATTATGAACT-TT-CTCTGGAAATGATGATCCATCA-ATTGATGAATTCAAG
2198866 TCTTTGCTAA
Statistics
Matches: 737, Mismatches: 12, Indels: 24
0.95 0.02 0.03
Matches are distributed among these distances:
114 303 0.41
115 14 0.02
116 21 0.03
117 42 0.06
118 33 0.04
119 324 0.44
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (116 bp):
GAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAATTGATGAATTCAAGCAAAA
GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
Found at i:2199574 original size:52 final size:52
Alignment explanation
Indices: 2199495--2199803 Score: 550
Period size: 52 Copynumber: 5.9 Consensus size: 52
2199485 TACTTGATTT
*
2199495 TGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
*
2199547 TGTCCAACCAGATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
2199599 TGAT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
1 TG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
* *
2199651 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCATAAGATGTTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
2199703 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
2199755 TGAT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
2199804 AGCACATTCA
Statistics
Matches: 247, Mismatches: 7, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
51 1 0.00
52 244 0.99
53 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (52 bp):
TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
Found at i:2200687 original size:19 final size:19
Alignment explanation
Indices: 2200665--2200701 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2200655 AATAGAAAAG
*
2200665 AATAAATTGAATTTCCAAA
1 AATAAATTGAATCTCCAAA
2200684 AATAAATTGAATCTCCAA
1 AATAAATTGAATCTCCAA
2200702 TAAGTTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (19 bp):
AATAAATTGAATCTCCAAA
Found at i:2201060 original size:17 final size:17
Alignment explanation
Indices: 2201040--2201074 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2201030 CTTGACCCCC
2201040 TTTTTTCGTT-TTTTTTT
1 TTTTTTC-TTCTTTTTTT
2201057 TTTTTTCTTCTTTTTTT
1 TTTTTTCTTCTTTTTTT
2201074 T
1 T
2201075 CTTCAAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.89
Consensus pattern (17 bp):
TTTTTTCTTCTTTTTTT
Found at i:2211660 original size:13 final size:15
Alignment explanation
Indices: 2211638--2211674 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2211628 TTTGACAGAA
2211638 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
2211650 AAATAAAATACTTGC
1 AAATAAAATACTTGC
2211665 AAATAAAATA
1 AAATAAAATA
2211675 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:2211713 original size:18 final size:17
Alignment explanation
Indices: 2211665--2211715 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
2211655 AAATACTTGC
*
2211665 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
2211683 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
2211701 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
2211716 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:2213262 original size:23 final size:23
Alignment explanation
Indices: 2213236--2213282 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2213226 CGTGACGGTT
2213236 GGGGCTCTCCGATGACAGGGTAA
1 GGGGCTCTCCGATGACAGGGTAA
2213259 GGGGCTCTCCGATGACAGGGTAA
1 GGGGCTCTCCGATGACAGGGTAA
2213282 G
1 G
2213283 CTTTTGTCTC
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:0.21, C:0.21, G:0.40, T:0.17
Consensus pattern (23 bp):
GGGGCTCTCCGATGACAGGGTAA
Found at i:2213849 original size:3 final size:3
Alignment explanation
Indices: 2213841--2213941 Score: 116
Period size: 3 Copynumber: 32.7 Consensus size: 3
2213831 TTAATATATT
*
2213841 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA AAA TAAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA-A TAA
* *
2213887 TAA T-A TTA TAA GTAA TAA TAAA TAT TAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA
2213934 TAA TAA TA
1 TAA TAA TA
2213942 TGGATAAAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
2 4 0.05
3 68 0.79
4 14 0.16
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2213887 original size:32 final size:32
Alignment explanation
Indices: 2213842--2213939 Score: 135
Period size: 32 Copynumber: 3.0 Consensus size: 32
2213832 TAATATATTT
*
2213842 AATAATAAAATAATAATAATAATAATAAAAATA
1 AATAAT-AAATAATAATAATAATAATAATAATA
* *
2213875 AATAATATATAATAAT-ATTATAAGTAATAATA
1 AATAATAAATAATAATAATAATAA-TAATAATA
*
2213907 AATATTAAATAATAATAATAATAATAATAATA
1 AATAATAAATAATAATAATAATAATAATAATA
2213939 A
1 A
2213940 TATGGATAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
31 6 0.11
32 39 0.68
33 12 0.21
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (32 bp):
AATAATAAATAATAATAATAATAATAATAATA
Found at i:2227711 original size:20 final size:20
Alignment explanation
Indices: 2227688--2227838 Score: 108
Period size: 20 Copynumber: 7.5 Consensus size: 20
2227678 GTTTCCAGAT
2227688 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
2227708 TCGCATTGCGATTTTCCGACTA
1 TCGCAATGCGA--TTCTGACTA
* * *
2227730 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* *
2227750 TCGCAATGCGAGTATGACTA
1 TCGCAATGCGATTCTGACTA
* * * *
2227770 TCGCAACGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
*
2227790 TCACAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
** * *
2227810 TCGCAACACGATTCTGGCTG
1 TCGCAATGCGATTCTGACTA
2227830 TCGCAATGC
1 TCGCAATGC
2227839 TGAATTTCAA
Statistics
Matches: 101, Mismatches: 24, Indels: 12
0.74 0.18 0.09
Matches are distributed among these distances:
19 2 0.02
20 79 0.78
21 2 0.02
22 18 0.18
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:2227781 original size:40 final size:40
Alignment explanation
Indices: 2227725--2227816 Score: 148
Period size: 40 Copynumber: 2.3 Consensus size: 40
2227715 GCGATTTTCC
* *
2227725 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAACGCGAATATGTAAATCACAATGCGAGTAT
* *
2227765 GACTATCGCAACGCGAATATGTAAATCACAATGCGATTCT
1 GACTATCGCAACGCGAATATGTAAATCACAATGCGAGTAT
2227805 GACTATCGCAAC
1 GACTATCGCAAC
2227817 ACGATTCTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (40 bp):
GACTATCGCAACGCGAATATGTAAATCACAATGCGAGTAT
Found at i:2228708 original size:24 final size:24
Alignment explanation
Indices: 2228657--2228710 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2228647 GTATTCGAAA
*
2228657 TTTGATCTTGGTCAATACCCGGAG
1 TTTGATCTTGGTCAATACCCAGAG
* *
2228681 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAG
2228705 TTTGAT
1 TTTGAT
2228711 GATATTTCAG
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:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAG
Found at i:2230982 original size:18 final size:18
Alignment explanation
Indices: 2230959--2230993 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2230949 AGCAAAAGGC
*
2230959 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
2230977 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
2230994 CAACCGGCTT
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:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:2231198 original size:20 final size:20
Alignment explanation
Indices: 2231173--2231412 Score: 161
Period size: 20 Copynumber: 12.6 Consensus size: 20
2231163 CATTCATTTA
*
2231173 ACTATCACAACGCAAATATG
1 ACTATCGCAACGCAAATATG
*
2231193 ACTATCGCAACACAAATATG
1 ACTATCGCAACGCAAATATG
*
2231213 ACTATCGCAACGCGAATATG
1 ACTATCGCAACGCAAATATG
** *
2231233 ACTATCGCAACGTGAATTTG
1 ACTATCGCAACGCAAATATG
* **
2231253 AATATCGCAACG---GGAT-
1 ACTATCGCAACGCAAATATG
*
2231269 A--ATCGCAATGCGAAA-ATG
1 ACTATCGCAACGC-AAATATG
* * *
2231287 ACTATCGCAACGCGAATTTT
1 ACTATCGCAACGCAAATATG
**
2231307 ACTATCGCAACG---GGAT-
1 ACTATCGCAACGCAAATATG
*
2231323 A--ATCGCAATGCGAAA-ATG
1 ACTATCGCAACGC-AAATATG
2231341 ACTATCGCAACGCGAAA-ATG
1 ACTATCGCAACGC-AAATATG
2231361 ACTATCGCAACGCGAAA-ATG
1 ACTATCGCAACGC-AAATATG
* *
2231381 ACTATCGCAACGCGAATTTG
1 ACTATCGCAACGCAAATATG
*
2231401 ACTATCACAACG
1 ACTATCGCAACG
2231413 AGAAAATTGC
Statistics
Matches: 179, Mismatches: 25, Indels: 32
0.76 0.11 0.14
Matches are distributed among these distances:
14 16 0.09
16 2 0.01
17 6 0.03
18 2 0.01
19 4 0.02
20 149 0.83
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
ACTATCGCAACGCAAATATG
Found at i:2231259 original size:40 final size:40
Alignment explanation
Indices: 2231173--2231412 Score: 225
Period size: 40 Copynumber: 6.3 Consensus size: 40
2231163 CATTCATTTA
* * * *
2231173 ACTATCACAACGCAAATATGACTATCGCAACACAAATATG
1 ACTATCGCAACGCGAATATGACTATCGCAACGCGAATATG
* *
2231213 ACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTG
1 ACTATCGCAACGCGAATATGACTATCGCAACGCGAATATG
* * * *
2231253 AATATCGCAACG-G--GAT-A--ATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAATATGACTATCGCAACGCGAATATG
* * *
2231287 ACTATCGCAACGCGAATTTTACTATCGCAACG-G--GAT-
1 ACTATCGCAACGCGAATATGACTATCGCAACGCGAATATG
* * *
2231323 A--ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAATATGACTATCGCAACGCGAATATG
* *
2231361 ACTATCGCAACGCGAAAATGACTATCGCAACGCGAATTTG
1 ACTATCGCAACGCGAATATGACTATCGCAACGCGAATATG
*
2231401 ACTATCACAACG
1 ACTATCGCAACG
2231413 AGAAAATTGC
Statistics
Matches: 162, Mismatches: 26, Indels: 24
0.76 0.12 0.11
Matches are distributed among these distances:
34 49 0.30
35 2 0.01
36 2 0.01
37 7 0.04
38 2 0.01
39 2 0.01
40 98 0.60
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (40 bp):
ACTATCGCAACGCGAATATGACTATCGCAACGCGAATATG
Found at i:2231282 original size:54 final size:54
Alignment explanation
Indices: 2231216--2231372 Score: 251
Period size: 54 Copynumber: 2.9 Consensus size: 54
2231206 AAATATGACT
* * * *
2231216 ATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
*
2231270 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTTACTATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
**
2231324 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACG
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACG
2231373 CGAAAATGAC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 95 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.20
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
Found at i:2231288 original size:74 final size:74
Alignment explanation
Indices: 2231210--2231455 Score: 241
Period size: 74 Copynumber: 3.3 Consensus size: 74
2231200 CAACACAAAT
* *
2231210 ATGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGCAACGGGATAATCGC
1 ATGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTGAATATCGCAACGAGATAATCGC
*
2231275 AATGCGAAA
66 AAAGCGAAA
* * * * * * *
2231284 ATGACTATCGCAACGCGAATTTTACTATCGCAACGGGATAATCGCA-AT-GCGAA-AATGACT-A
1 ATGACTATCGCAACGCGAATATGACTATCGCAACGCGA-ATTTGAATATCGC-AACGA-GA-TAA
*
2231345 TCGCAACGCGAAA
62 TCGCAAAGCGAAA
* * * * *
2231358 ATGACTATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCACAACGAGAAAATTGC
1 ATGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTGAATATCGCAACGAGATAATCGC
* *
2231423 AAAGTG-TA
66 AAAGCGAAA
*
2231431 TTAGACTATCGCAACGCGAATATGA
1 AT-GACTATCGCAACGCGAATATGA
2231456 TGCAGATTGA
Statistics
Matches: 137, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
73 7 0.05
74 123 0.90
75 7 0.05
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (74 bp):
ATGACTATCGCAACGCGAATATGACTATCGCAACGCGAATTTGAATATCGCAACGAGATAATCGC
AAAGCGAAA
Found at i:2231438 original size:94 final size:94
Alignment explanation
Indices: 2231270--2231455 Score: 257
Period size: 94 Copynumber: 2.0 Consensus size: 94
2231260 CAACGGGATA
* * * * * *
2231270 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTTACTATCGCAACGGGATAATCGCAATGCG
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCACAACGAGAAAATCGCAAAGCG
2231335 AAAATGACTATCGCAACGCGAAAATGACT
66 AAAATGACTATCGCAACGCGAAAATGACT
* *
2231364 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCACAACGAGAAAATTGCAAAGTG
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCACAACGAGAAAATCGCAAAGCG
* * *
2231429 -TATTAGACTATCGCAACGCGAATATGA
66 AAAAT-GACTATCGCAACGCGAAAATGA
2231456 TGCAGATTGA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 2 0.03
94 78 0.98
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (94 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCACAACGAGAAAATCGCAAAGCG
AAAATGACTATCGCAACGCGAAAATGACT
Found at i:2231587 original size:36 final size:34
Alignment explanation
Indices: 2231547--2231626 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 34
2231537 TCAACTTTTA
2231547 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
2231583 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
*
2231613 ATTAATTAAACAAA
1 ATCAATTAAACAAA
2231627 TCAACTCTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
30 27 0.69
32 2 0.05
34 3 0.08
36 7 0.18
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.28
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:2231596 original size:30 final size:30
Alignment explanation
Indices: 2231562--2231627 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
2231552 TTAAACAAGC
2231562 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
*
2231592 ACAAATAAGAATTATTTACACATTAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
2231622 ACAAAT
1 ACAAAT
2231628 CAACTCTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:2233120 original size:42 final size:42
Alignment explanation
Indices: 2233022--2233120 Score: 94
Period size: 42 Copynumber: 2.4 Consensus size: 42
2233012 TTGGGAGGGA
* * * **
2233022 CCTCTTCAACGATGACAGTGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAAAGTGGCCTCTTGAACGATGGGAGAAG
* **
2233064 ACTCTTGAGGGATGATAAG-GGCCTCTTGAACGATAGGG-GAAG
1 CCTCTTGAACGATGA-AAGTGGCCTCTTGAACGAT-GGGAGAAG
2233106 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
2233121 CAGGTGAGTC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
42 39 0.89
43 5 0.11
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (42 bp):
CCTCTTGAACGATGAAAGTGGCCTCTTGAACGATGGGAGAAG
Found at i:2233648 original size:20 final size:20
Alignment explanation
Indices: 2233623--2233696 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
2233613 GCAACACAAG
*
2233623 TGACTATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAAAA
*
2233643 TGACTATCACAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
**
2233663 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAAAA
2233683 TGACTATCGCAACG
1 TGACTATCGCAACG
2233697 AGAGAATCGC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
TGACTATCGCAACGCGAAAA
Found at i:2233764 original size:20 final size:20
Alignment explanation
Indices: 2233739--2233786 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2233729 GCGATTCTTT
2233739 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCC
* ** *
2233759 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCC
2233779 CGTTGCGA
1 CGTTGCGA
2233787 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCC
Found at i:2235716 original size:20 final size:20
Alignment explanation
Indices: 2235693--2235799 Score: 110
Period size: 20 Copynumber: 5.5 Consensus size: 20
2235683 TCTGAAACTT
*
2235693 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
*
2235713 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
2235733 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
2235753 ATTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
* *
2235772 AAAATCACAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
2235791 AAAATCGCA
1 AAAATCGCA
2235800 TTGCGATTCT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
19 22 0.30
20 51 0.70
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:2236173 original size:22 final size:22
Alignment explanation
Indices: 2236145--2236197 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
2236135 TTCTGACCGT
2236145 GATGGGGACTGATTTCGTCGGA
1 GATGGGGACTGATTTCGTCGGA
2236167 GATGGGGACTGATTTCGTCGGA
1 GATGGGGACTGATTTCGTCGGA
2236189 GATGGGGAC
1 GATGGGGAC
2236198 GAATGTCGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.13, G:0.43, T:0.25
Consensus pattern (22 bp):
GATGGGGACTGATTTCGTCGGA
Found at i:2236404 original size:35 final size:35
Alignment explanation
Indices: 2236362--2236429 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
2236352 GATAATAATG
2236362 GCGCTTTGAAAATCGCATTGCGACAGTCAGAATTA
1 GCGCTTTGAAAATCGCATTGCGACAGTCAGAATTA
2236397 GCGCTTTGAAAATCGCATTGCGACAGTCAGAAT
1 GCGCTTTGAAAATCGCATTGCGACAGTCAGAAT
2236430 CGCGTTGCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (35 bp):
GCGCTTTGAAAATCGCATTGCGACAGTCAGAATTA
Found at i:2236432 original size:20 final size:20
Alignment explanation
Indices: 2236407--2236602 Score: 119
Period size: 20 Copynumber: 9.7 Consensus size: 20
2236397 GCGCTTTGAA
*
2236407 AATCGCATTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAG
*
2236427 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
2236447 AATCGCATTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * * *
2236467 ACTTGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* * *
2236487 ATTCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
2236507 ACTCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* *
2236527 ATTCGCATTGCGATAGTCGAAA
1 AATCGCATTGCGATAGTC--AG
** * * *
2236549 AATCGCAACGCGA-ATTTGGAA
1 AATCGCATTGCGATA-GT-CAG
*
2236570 AATCGCAATGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
2236590 AATCGCGTTGCGA
1 AATCGCATTGCGA
2236603 ATCTGGAAAC
Statistics
Matches: 139, Mismatches: 28, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.01
20 106 0.76
21 18 0.13
22 13 0.09
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:2236465 original size:40 final size:40
Alignment explanation
Indices: 2236407--2236602 Score: 169
Period size: 40 Copynumber: 4.8 Consensus size: 40
2236397 GCGCTTTGAA
* * * *
2236407 AATCGCATTGCGACAGTCAGAATCGCGTTGCGATAGT-CAG
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGAT-TTACAT
* * *
2236447 AATCGCATTGCGATAGTCATACTTGCATTGCGATTTACAT
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGATTTACAT
* * * *
2236487 ATTCGCGTTGCGATAGTCATACTCGCATTGCGATTTACAT
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGATTTACAT
* * ** ** *
2236527 ATTCGCATTGCGATAGTCGAAAAATCGCAACGCGAATTTGGAA
1 AATCGCATTGCGATAGTC--AGAATCGCATTGCG-ATTTACAT
* *
2236570 AATCGCAATGCGATAGTCAGAATCGCGTTGCGA
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGA
2236603 ATCTGGAAAC
Statistics
Matches: 128, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 86 0.67
41 10 0.08
42 10 0.08
43 21 0.16
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCAGAATCGCATTGCGATTTACAT
Found at i:2236561 original size:22 final size:22
Alignment explanation
Indices: 2236536--2236587 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
2236526 TATTCGCATT
2236536 GCGATAGTCGAAAAATCGCAAC
1 GCGATAGTCGAAAAATCGCAAC
* * * *
2236558 GCGA-ATTTGGAAAATCGCAAT
1 GCGATAGTCGAAAAATCGCAAC
2236579 GCGATAGTC
1 GCGATAGTC
2236588 AGAATCGCGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (22 bp):
GCGATAGTCGAAAAATCGCAAC
Found at i:2239827 original size:33 final size:33
Alignment explanation
Indices: 2239790--2239861 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
2239780 CTAGAGAATA
2239790 TTTTCT-TAATTTTTATTTATTTAATCTAATAAT
1 TTTTCTGT-ATTTTTATTTATTTAATCTAATAAT
2239823 TTTTCTGTATTTTTATTTATTTAATCTAATAAT
1 TTTTCTGTATTTTTATTTATTTAATCTAATAAT
2239856 TTTTCT
1 TTTTCT
2239862 ATCCAATAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 37 0.97
34 1 0.03
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.65
Consensus pattern (33 bp):
TTTTCTGTATTTTTATTTATTTAATCTAATAAT
Found at i:2251271 original size:23 final size:23
Alignment explanation
Indices: 2251217--2251271 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
2251207 AGATTTAATT
* * *
2251217 TAAATAAAATTTAAAAAGATAAA
1 TAAATAATATTAAAAAACATAAA
*
2251240 TAAAATAATATTAAAAAACTTAAA
1 T-AAATAATATTAAAAAACATAAA
2251264 TAAATAAT
1 TAAATAAT
2251272 TTTATTACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
TAAATAATATTAAAAAACATAAA
Found at i:2254112 original size:44 final size:44
Alignment explanation
Indices: 2254046--2254129 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
2254036 GTGAACAAAC
* *
2254046 TTCACAAGCTTACATTTGTTAAAATATATATTCTCTTTGTAAGT
1 TTCACAAGCTTACATTTATTAAAATATATATTATCTTTGTAAGT
*
2254090 TTCACAAGCTTGCATTTATTAAAATATATATTATCTTTGT
1 TTCACAAGCTTACATTTATTAAAATATATATTATCTTTGT
2254130 TTTTGTTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.46
Consensus pattern (44 bp):
TTCACAAGCTTACATTTATTAAAATATATATTATCTTTGTAAGT
Found at i:2254570 original size:3 final size:3
Alignment explanation
Indices: 2254503--2254557 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
2254493 TTCATTTGAA
2254503 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2254548 T-T TAT TAT TA
1 TAT TAT TAT TA
2254558 ATAAATATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 3 0.06
3 45 0.92
4 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2255873 original size:3 final size:3
Alignment explanation
Indices: 2255865--2255894 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2255855 TTTACTTTTA
*
2255865 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2255895 TAACCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2256110 original size:20 final size:19
Alignment explanation
Indices: 2256085--2256126 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2256075 TTATTTTATA
2256085 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
2256105 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
2256124 AAT
1 AAT
2256127 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:2260055 original size:15 final size:15
Alignment explanation
Indices: 2260035--2260066 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2260025 GATCAATACC
2260035 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
2260050 TTTTGCATACATTCA
1 TTTTGCATACATGCA
2260065 TT
1 TT
2260067 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:2267406 original size:14 final size:13
Alignment explanation
Indices: 2267389--2267439 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
2267379 ATGCTTGAAA
2267389 AATAAAATGAAAAG
1 AATAAAA-GAAAAG
2267403 AATAAAAGAAAAAG
1 AATAAAAG-AAAAG
*
2267417 AA-AAAA-AGAAG
1 AATAAAAGAAAAG
*
2267428 AAAAAAAGAAAA
1 AATAAAAGAAAA
2267440 AAAAGAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 6 0.19
12 4 0.12
13 8 0.25
14 14 0.44
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (13 bp):
AATAAAAGAAAAG
Found at i:2267433 original size:19 final size:19
Alignment explanation
Indices: 2267411--2267455 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2267401 AGAATAAAAG
2267411 AAAAAG-AAAAAAAGAAGAA
1 AAAAAGAAAAAAAAG-AGAA
2267430 AAAAAGAAAAAAAAGAGAA
1 AAAAAGAAAAAAAAGAGAA
2267449 AAAAAGA
1 AAAAAGA
2267456 GGGGGTCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAAAAGAGAA
Found at i:2267850 original size:19 final size:17
Alignment explanation
Indices: 2267808--2267856 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
2267798 TATTTTCTCT
2267808 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
2267824 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
*
2267842 AAAATTCAACTTATT
1 -AAATTCAATTTATT
2267857 CTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 1 0.04
19 12 0.44
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:2268375 original size:114 final size:114
Alignment explanation
Indices: 2268170--2268392 Score: 347
Period size: 114 Copynumber: 2.0 Consensus size: 114
2268160 TGCCACGTTA
* * * *
2268170 TCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATAG
* * * *
2268235 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTCGGTAAGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGC
* *
2268284 TCATAGTAGAAATAAGAAGACCCATTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATAG
*
2268349 TTCGGTAAGAACCCCAGAACCAATCATTAGAATTGAAAGATGAA
66 TTCGGTAAGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
2268393 CTGCATGATC
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATAG
TTCGGTAAGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGC
Found at i:2269291 original size:110 final size:110
Alignment explanation
Indices: 2269150--2269882 Score: 751
Period size: 110 Copynumber: 6.5 Consensus size: 110
2269140 ACAACTCATT
*
2269150 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATT
1 TGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATT
* * *
2269215 CGATGGATCATCATTGCCAGAAGGTTCATAATAAGAAGAACATATC
65 CGATGGATCAACATTGCCAGAAGGTTCATAATGAGAAGAACTTATC
*
2269261 TGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTC
1 TGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTC
* *
2269326 GATGGATCAACGTTGCCAGAAGGTTCATAATGATAAGAACTTATC
66 GATGGATCAACATTGCCAGAAGGTTCATAATGAGAAGAACTTATC
** * * *
2269371 AT-CTGAGGAAGATGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTTGCTTG-ATTCTATCA
1 -TGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTTGCTTGAATTC-AT--
* * * * * ** *
2269434 CAGAAAAAGATAGATCAGCATTAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATC
61 C------A-TTCGAT--GGATCAACATTGCCAG-AAG-GTTCATAATGAGAAGAACTTATC
* ** * *
2269495 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAATTTTTGTTTAAATTCATCATT
1 TGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATT
* * * *
2269560 CGATGGATCATCATTTCAAGAGAAAGTTCATAATGAGAAGAACTTATC
65 CGATGGATCAACATTGC--CAGAAGGTTCATAATGAGAAGAACTTATC
* *
2269608 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGA-TTGTTCAACCTTTTGTTTAAATTCATCAT
1 TGAAG-AGGAAGAAGAAGTTCATAATGAGAAGA-ACTTGTTCAACCTTTTGCTTGAATTCATCAT
* *
2269672 TTGATTGATCAACATTGCCAGGTATA-GTTCATAATGAGAAGAACTCGTCATC
64 TCGATGGATCAACATTGCCA-G-A-AGGTTCATAATGAGAAGAACT--T-ATC
* * * * *
2269724 TG-A-A-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCACTC
1 TGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTC
* * *
2269786 GATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATC
66 GATGGATCAACATTGCC--AGAAGGTTCATAATGAGAAGAACTTATC
* * *
2269833 TGAAGAAGAAGAAGAAGTTCGTAATGAGAAGAGCTTGTTCAACCTTTTGC
1 TGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
2269883 ATAACTCTAT
Statistics
Matches: 525, Mismatches: 62, Indels: 69
0.80 0.09 0.11
Matches are distributed among these distances:
109 5 0.01
110 143 0.27
111 20 0.04
112 123 0.23
113 129 0.25
114 3 0.01
115 8 0.02
116 6 0.01
119 1 0.00
120 4 0.01
122 13 0.02
123 2 0.00
124 31 0.06
125 37 0.07
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (110 bp):
TGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTC
GATGGATCAACATTGCCAGAAGGTTCATAATGAGAAGAACTTATC
Found at i:2269770 original size:225 final size:225
Alignment explanation
Indices: 2269471--2269881 Score: 686
Period size: 225 Copynumber: 1.8 Consensus size: 225
2269461 TTCCAGTTCG
2269471 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
2269536 AAATTTTTGTTTAAATTCATCATTCGATGGATCATCATTTCAAGAGAAAGTTCATAATGAGAAGA
66 AAATTTTTGTTTAAATTCATCACTCGATGGATCAACATTTCAAGAGAAAGTTCATAATGAGAAGA
2269601 ACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGATTGTTCAACCTTTTGTTTAAATT
131 ACTTATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAGATTGTTCAACCTTTTGTTTAAATT
2269666 CATCATTTGATTGATCAACATTGCCAGGTAT
195 CATCATTTGATTGATCAACATTGCCAGGTAT
2269697 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-TTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* * * *
2269758 TTCAACTTTTTGTTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGA
63 TTCAAATTTTTGTTTAAATTCATCACTCGATGGATCAACATTTCAAGAGAAAGTTCATAATGAGA
* *
2269823 AGAACTTATCTGAAGAAGAAGAAGAAGTTCGTAATGAGAAGAGCTTGTTCAACCTTTTG
128 AGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGATTGTTCAACCTTTTG
2269882 CATAACTCTA
Statistics
Matches: 174, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
224 40 0.23
225 96 0.55
226 20 0.11
227 1 0.01
228 5 0.03
229 12 0.07
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (225 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AAATTTTTGTTTAAATTCATCACTCGATGGATCAACATTTCAAGAGAAAGTTCATAATGAGAAGA
ACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGATTGTTCAACCTTTTGTTTAAATTC
ATCATTTGATTGATCAACATTGCCAGGTAT
Found at i:2269778 original size:112 final size:113
Alignment explanation
Indices: 2269471--2269881 Score: 584
Period size: 113 Copynumber: 3.7 Consensus size: 113
2269461 TTCCAGTTCG
*
2269471 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
** * *
2269536 AAATTTTTGTTTAAATTCATCATTCGATGGATCATCATTTCAAGAGAA
66 AACCTTTTGTTTAAATTCATCATTCGATGGATCAACATTTCCAGAGAA
2269584 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGA-TTGTT
1 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA-ATTTGTT
* * * *
2269648 CAACCTTTTGTTTAAATTCATCATTTGATTGATCAACATTGCCAG-GTAT
65 CAACCTTTTGTTTAAATTCATCATTCGATGGATCAACATTTCCAGAG-AA
2269697 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-TTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACT--T-ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* * * *
2269758 TTCAACTTTTTGTTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGAA
63 TTCAACCTTTTGTTTAAATTCATCATTCGATGGATCAACATTTCCAGAGAA
* **
2269809 AGTTCATAATGAGAAGAACTTATCTGAAGAA-GAAGAAGAAGTTCGTAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
2269873 AACCTTTTG
66 AACCTTTTG
2269882 CATAACTCTA
Statistics
Matches: 267, Mismatches: 21, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
109 14 0.05
110 2 0.01
111 3 0.01
112 108 0.40
113 123 0.46
114 2 0.01
115 5 0.02
116 10 0.04
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGTTTAAATTCATCATTCGATGGATCAACATTTCCAGAGAA
Found at i:2269951 original size:348 final size:338
Alignment explanation
Indices: 2269105--2269886 Score: 868
Period size: 348 Copynumber: 2.3 Consensus size: 338
2269095 CATTTAATGG
* ** * * *
2269105 ATCAACATTTTCAGTTAGAGTTCATAATAAGAAGAACAACTCATTTGAAGAAGGAAGAAGAAGTT
1 ATCAACATTTCCAGAGAAAGTTCATAAT--G-AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * *
2269170 CATAATGAGAAGAACTTGTTCAACCTTTTGC-TCGAATTCATCATTCGATGGATCATCAT-TGC-
63 CATAATGAGAAGAACTTGTTCAAACTTTTGCAT-AAATTCATCA-TCGAGGGATCATCATAT-CA
* * * *
2269232 -CAGAAGGTTCATAATAAGAAGAACATATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAAC
125 AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * *
2269295 TTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCAACGTTGCCAGAAGGTTCATAATGAT
190 TTGTTCAACCTTTTGCTCAAATTCATCATTCGATGGATCAACATTGCCAGAAGGTTCATAATGAG
* * * * *
2269360 AAGAACTTATCATCTGAGGAAGATGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTTGCTTG
255 AAGAACTCATCATCTGAAGAAGAAGAAATTCACAATGAGAAGAACTTGTTCAACCTTTTTGCTTG
2269425 ATTCTATCACAGAAAAAGATAGATCAGC
320 ATTCTATCAC--------ATAGAT-AGC
* ****
2269453 ATTAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * ** * *
2269518 AATGAGAAGAATTTGTTCAAATTTTTGTTTAAATTCATCATTCGATGGATCATCATTTCAAGAGA
66 AATGAGAAGAACTTGTTCAAACTTTTGCATAAATTCATCA-TCGAGGGATCATCATATCAAGAGA
2269583 AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGA-TTGT
130 AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA-ACTTGT
* * * *
2269647 TCAACCTTTTGTTTAAATTCATCATTTGATTGATCAACATTGCCAGGTATA-GTTCATAATGAGA
194 TCAACCTTTTGCTCAAATTCATCATTCGATGGATCAACATTGCCA-G-A-AGGTTCATAATGAGA
* * * *
2269711 AGAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-CTTTTTGTTTGA
256 AGAACTCATCATCTGAAGAAGAAGAAATTCACAATGAGAAGAACTTGTTCAACCTTTTTGCTTG-
* *
2269775 ATTC-ATCAC-TCGAT-GG
320 ATTCTATCACATAGATAGC
* * *
2269791 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAA-GAAGAAGAAGTTCGT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
2269855 AATGAGAAGAGCTTGTTCAACCTTTTGCATAA
66 AATGAGAAGAACTTGTTCAAACTTTTGCATAA
2269887 CTCTATCACA
Statistics
Matches: 378, Mismatches: 46, Indels: 31
0.83 0.10 0.07
Matches are distributed among these distances:
337 40 0.11
338 43 0.11
340 4 0.01
345 84 0.22
346 3 0.01
347 30 0.08
348 95 0.25
349 17 0.04
350 61 0.16
351 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (338 bp):
ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAAACTTTTGCATAAATTCATCATCGAGGGATCATCATATCAAGAGAA
AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTCAAATTCATCATTCGATGGATCAACATTGCCAGAAGGTTCATAATGAGAAGAAC
TCATCATCTGAAGAAGAAGAAATTCACAATGAGAAGAACTTGTTCAACCTTTTTGCTTGATTCTA
TCACATAGATAGC
Found at i:2270301 original size:3 final size:3
Alignment explanation
Indices: 2270219--2270288 Score: 99
Period size: 3 Copynumber: 23.7 Consensus size: 3
2270209 TTCGATTGAA
* *
2270219 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT AAT TAT CAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2270264 TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2270289 ATAAATATTA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 3 0.05
3 56 0.93
4 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2271613 original size:3 final size:3
Alignment explanation
Indices: 2271605--2271640 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
2271595 TTTACTTTTA
* *
2271605 ATT ATT ATT ACT GTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2271641 TAACCATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2277847 original size:25 final size:24
Alignment explanation
Indices: 2277819--2277899 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 24
2277809 TTCAAATAAC
*
2277819 TTCATCAAACATTTTTCAAAATTCT
1 TTCATCAAAAATTTTT-AAAATTCT
** *
2277844 TTCATCAAATTTTTTTTAAAGTTCT
1 TTCATCAAA-AATTTTTAAAATTCT
* *
2277869 TTCATAAAAAAAATATTTAAAATTCT
1 TTCAT--CAAAAATTTTTAAAATTCT
2277895 TTCAT
1 TTCAT
2277900 TATATAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
25 21 0.47
26 21 0.47
27 3 0.07
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.47
Consensus pattern (24 bp):
TTCATCAAAAATTTTTAAAATTCT
Found at i:2278430 original size:20 final size:19
Alignment explanation
Indices: 2278386--2278430 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2278376 AAAATGTTTT
* *
2278386 TATGAATAGTATTATACTG
1 TATGAATAGTATGATACTA
2278405 TATGAATAGTACTGATACTA
1 TATGAATAGTA-TGATACTA
*
2278425 TGTGAA
1 TATGAA
2278431 CAATAATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (19 bp):
TATGAATAGTATGATACTA
Found at i:2279925 original size:17 final size:18
Alignment explanation
Indices: 2279897--2279938 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2279887 GATGTTGAAG
* *
2279897 GAAGAGGAAAAATATGAA
1 GAAGAAGAAAAATAAGAA
2279915 G-AGAAGAAAAATAAGAA
1 GAAGAAGAAAAATAAGAA
2279932 GAAGAAG
1 GAAGAAG
2279939 GGGGAGGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (18 bp):
GAAGAAGAAAAATAAGAA
Found at i:2281631 original size:20 final size:21
Alignment explanation
Indices: 2281606--2281652 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2281596 TTAACAAGTA
2281606 TATTTT-TTAACAATTGATAT
1 TATTTTGTTAACAATTGATAT
2281626 TATTTTGTTAACAATTGATAT
1 TATTTTGTTAACAATTGATAT
*
2281647 CATTTT
1 TATTTT
2281653 CATTAAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (21 bp):
TATTTTGTTAACAATTGATAT
Found at i:2281904 original size:20 final size:20
Alignment explanation
Indices: 2281865--2281934 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
2281855 AATGTTTTTT
2281865 TATGAATAGTATTG-TATTG
1 TATGAATAGTATTGATATTG
*
2281884 TATGAATAGTATCGATATTG
1 TATGAATAGTATTGATATTG
*
2281904 TATGAATAGTATTGATACTG
1 TATGAATAGTATTGATATTG
* *
2281924 TGTGAACAGTA
1 TATGAATAGTA
2281935 ATGAATATAC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 13 0.29
20 32 0.71
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.40
Consensus pattern (20 bp):
TATGAATAGTATTGATATTG
Found at i:2281995 original size:20 final size:20
Alignment explanation
Indices: 2281966--2282013 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2281956 AATTCCAGAA
*
2281966 TGCTACAGGGGTATCGATAC
1 TGCTACAGGGGTACCGATAC
* *
2281986 TGCTATAGGGGTACCGATAT
1 TGCTACAGGGGTACCGATAC
2282006 TGCTACAG
1 TGCTACAG
2282014 TAATTTCAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
TGCTACAGGGGTACCGATAC
Found at i:2283308 original size:23 final size:23
Alignment explanation
Indices: 2283275--2283335 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
2283265 TCGTATAAAG
*
2283275 GCACCGAAGTGCCATGTAGAATT
1 GCACCGAAGTGCCATGTAGAAAT
* **
2283298 GCACCGTAGTGCCGCGTAGAAAT
1 GCACCGAAGTGCCATGTAGAAAT
*
2283321 GTACCGAAGTGCCAT
1 GCACCGAAGTGCCAT
2283336 ATAATAATGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
GCACCGAAGTGCCATGTAGAAAT
Found at i:2284735 original size:21 final size:21
Alignment explanation
Indices: 2284711--2284755 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2284701 TTTTGTTCGT
* *
2284711 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2284732 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2284753 TTG
1 TTG
2284756 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2286390 original size:217 final size:217
Alignment explanation
Indices: 2285963--2286493 Score: 715
Period size: 217 Copynumber: 2.4 Consensus size: 217
2285953 CATAAGAGGC
* ** * *
2285963 CAGATTCTCTTCTTTATGGATGAGCAATGAT-GTTTTTCAACACCAAATTATCTCCAGACAATCA
1 CAGATTCTCTTCATCGTGGATGAACAATG-TCG-TTTTCAACACCAAATTATCTCCAGGCAATCA
* * * * * *
2286027 GATTTTCTAAACAAGAAGGAACATTGTTGTCTTCAGATGCGATTAGATTTCCTCATCAAGTAAGA
64 GATTTCCTCAACAAGAAGGAACAATGTTGTCTTCAAATGCGACTAGATTTCCTCATCAAGCAAGA
* * * *
2286092 ACAATGTCGTCCGCTGACTAGACCTCCTCAACATGAAGGAGAAACGTCAGCACTAGATTTGATAT
129 ACAATGTCGTCCGCCGACTAAACCTCCTCAACATGAAGAAGAAACGTCAGCACCAGATTTGATAT
2286157 CGAACAAATCACCCCAAAGGTGGT
194 CGAACAAATCACCCCAAAGGTGGT
* *
2286181 CAGATTCTCTTCATCGTGGATGAACAATGTCGTTTTCAACACGAAATTATCTCTAGGCAATCAGA
1 CAGATTCTCTTCATCGTGGATGAACAATGTCGTTTTCAACACCAAATTATCTCCAGGCAATCAGA
* *
2286246 TTTCCTCAACAAGAAAGAACAGTGTTGTCTTCAAATGCGACTAGATTTCCTCATCAAGCAAGAAC
66 TTTCCTCAACAAGAAGGAACAATGTTGTCTTCAAATGCGACTAGATTTCCTCATCAAGCAAGAAC
* * * *
2286311 AATGTTGTCCGCCGACTAAACCTCCTCAACATGAAGAAGCAATGTCAGCACCAGATTT-TTCATC
131 AATGTCGTCCGCCGACTAAACCTCCTCAACATGAAGAAGAAACGTCAGCACCAGATTTGAT-ATC
* *
2286375 GAGCAAATTACCCCAAAGGTGGT
195 GAACAAATCACCCCAAAGGTGGT
** * * * ** *
2286398 CAGATTCTCTTCATCGTGGATGATTAGTGTCATTTCCAACATTAAATTATCTCCAAGCAATCAGA
1 CAGATTCTCTTCATCGTGGATGAACAATGTCGTTTTCAACACCAAATTATCTCCAGGCAATCAGA
*
2286463 TTTCCTCAACAAGAAGGAACAAAGTTGTCTT
66 TTTCCTCAACAAGAAGGAACAATGTTGTCTT
2286494 TAGATGCATA
Statistics
Matches: 275, Mismatches: 36, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
216 1 0.00
217 248 0.90
218 26 0.09
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (217 bp):
CAGATTCTCTTCATCGTGGATGAACAATGTCGTTTTCAACACCAAATTATCTCCAGGCAATCAGA
TTTCCTCAACAAGAAGGAACAATGTTGTCTTCAAATGCGACTAGATTTCCTCATCAAGCAAGAAC
AATGTCGTCCGCCGACTAAACCTCCTCAACATGAAGAAGAAACGTCAGCACCAGATTTGATATCG
AACAAATCACCCCAAAGGTGGT
Found at i:2286918 original size:32 final size:32
Alignment explanation
Indices: 2286882--2286965 Score: 114
Period size: 36 Copynumber: 2.5 Consensus size: 32
2286872 TTGAAATGAA
*
2286882 AATATCTTTTGAAATTTTATTTCGCATGAGAT
1 AATATCTTTTGAAATTTTATCTCGCATGAGAT
2286914 AATATCTTTTGAAATTAATTTTATCTCGCATGAGAT
1 AATATCTTTTG--A--AATTTTATCTCGCATGAGAT
*
2286950 AATATATTTTGAAATT
1 AATATCTTTTGAAATT
2286966 AATTTTATCT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
32 15 0.33
34 2 0.04
36 29 0.63
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (32 bp):
AATATCTTTTGAAATTTTATCTCGCATGAGAT
Found at i:2286943 original size:36 final size:36
Alignment explanation
Indices: 2286894--2286976 Score: 148
Period size: 36 Copynumber: 2.3 Consensus size: 36
2286884 TATCTTTTGA
* *
2286894 AATTTTATTTCGCATGAGATAATATCTTTTGAAATT
1 AATTTTATCTCGCATGAGATAATATATTTTGAAATT
2286930 AATTTTATCTCGCATGAGATAATATATTTTGAAATT
1 AATTTTATCTCGCATGAGATAATATATTTTGAAATT
2286966 AATTTTATCTC
1 AATTTTATCTC
2286977 CCTTGACTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.47
Consensus pattern (36 bp):
AATTTTATCTCGCATGAGATAATATATTTTGAAATT
Found at i:2296915 original size:31 final size:31
Alignment explanation
Indices: 2296892--2297001 Score: 184
Period size: 31 Copynumber: 3.5 Consensus size: 31
2296882 CATAGATTCG
* * *
2296892 GAAGAACCTAAGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
2296923 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
2296954 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
2296985 TAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
2297002 CCTCGACCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:2298835 original size:32 final size:33
Alignment explanation
Indices: 2298769--2298839 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 33
2298759 ATAACATTAT
* *
2298769 TAATTATTTATTATATTTAATATTTTACACATA
1 TAATTATTTATTATATTTAATAATTTACAAATA
2298802 TAATT-TTTCATTAT-TTTAA-AATTTACAAA-A
1 TAATTATTT-ATTATATTTAATAATTTACAAATA
2298832 TATATTAT
1 TA-ATTAT
2298840 AATTTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
30 3 0.09
31 11 0.33
32 9 0.27
33 10 0.30
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (33 bp):
TAATTATTTATTATATTTAATAATTTACAAATA
Found at i:2298874 original size:16 final size:15
Alignment explanation
Indices: 2298854--2298900 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
2298844 TTTTTATAAA
2298854 ATATATATTTTAATT
1 ATATATATTTTAATT
*
2298869 ACTATAT-TTATATATT
1 A-TATATATTTTA-ATT
2298885 AT-TATATTTTAATT
1 ATATATATTTTAATT
2298899 AT
1 AT
2298901 TTATTGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.30
15 10 0.37
16 9 0.33
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATATATTTTAATT
Found at i:2298901 original size:14 final size:14
Alignment explanation
Indices: 2298857--2298905 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
2298847 TTATAAAATA
*
2298857 TATATTTTAATTAC
1 TATATTTTAATTAT
2298871 TATATTTATATATTAT
1 TATATTT-TA-ATTAT
2298887 TATATTTTAATTAT
1 TATATTTTAATTAT
2298901 T-TATT
1 TATATT
2298906 GAATTTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 4 0.12
14 13 0.41
15 4 0.12
16 11 0.34
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TATATTTTAATTAT
Found at i:2299598 original size:22 final size:22
Alignment explanation
Indices: 2299570--2299622 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
2299560 ATTTTTAATT
*
2299570 ACATGTAACTAAAATATAGCTA
1 ACATGTAACTAAAATATAACTA
2299592 ACATGTAACTAAAATATAACTA
1 ACATGTAACTAAAATATAACTA
2299614 ACATGTAAC
1 ACATGTAAC
2299623 ATTAGGCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (22 bp):
ACATGTAACTAAAATATAACTA
Found at i:2299603 original size:11 final size:11
Alignment explanation
Indices: 2299570--2299622 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
2299560 ATTTTTAATT
2299570 ACATGTAACTA
1 ACATGTAACTA
* * *
2299581 AAATATAGCTA
1 ACATGTAACTA
2299592 ACATGTAACTA
1 ACATGTAACTA
* *
2299603 AAATATAACTA
1 ACATGTAACTA
2299614 ACATGTAAC
1 ACATGTAAC
2299623 ATTAGGCATG
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (11 bp):
ACATGTAACTA
Found at i:2299834 original size:20 final size:20
Alignment explanation
Indices: 2299805--2299854 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2299795 GGTGGCGAAA
2299805 ATAA-AATTTTTAAAAA-AT
1 ATAATAATTTTTAAAAATAT
**
2299823 ATATATAATTTTTTTAAATAT
1 ATA-ATAATTTTTAAAAATAT
2299844 ATAATAATTTT
1 ATAATAATTTT
2299855 AAGATTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 1 0.04
20 18 0.67
21 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATAATTTTTAAAAATAT
Found at i:2299854 original size:17 final size:17
Alignment explanation
Indices: 2299823--2299856 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2299813 TTTAAAAAAT
**
2299823 ATATATAATTTTTTTAA
1 ATATATAATAATTTTAA
2299840 ATATATAATAATTTTAA
1 ATATATAATAATTTTAA
2299857 GATTTCAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATAATAATTTTAA
Found at i:2302870 original size:149 final size:147
Alignment explanation
Indices: 2302627--2303016 Score: 505
Period size: 149 Copynumber: 2.6 Consensus size: 147
2302617 TGACGAGTAT
* * *
2302627 TGATGGGGCACTAAAAAGTTGCTT-GCATTTTATT-CATGATGCATTATTAATGGCATTTCATGA
1 TGAT-GGGCACTAAAAAGTTG-TTGGCATTTTTTTGCATGATGCATTATTAATGACATTTTATGA
* * * *
2302690 AGATTATTAATGACTCGTTTTAACATTTTCGGGCATGGTGCATTATTAGAGATGACATTTCACTA
64 AGATTATTAATGGCTCGTTTTGACATTTTCGGGCATAGTGCATTATTAGAGATAACATTTCACTA
*
2302755 AAAAGTTGCTGAAGATGAC
129 AAAAGTTGCTAAAGATGAC
* * **
2302774 TGATAGGGCACTGAAAAGTTGTTGGCATTTTTTTAGCATGGTGCATTATTAATGTTATTTTATGA
1 TGAT-GGGCACTAAAAAGTTGTTGGCATTTTTTT-GCATGATGCATTATTAATGACATTTTATGA
* * * *
2302839 AAATTATTAATGGCCCGTTTTGACATTTTCGGGCATAGTGCATTATTAGAGATAACATTTCATTG
64 AGATTATTAATGGCTCGTTTTGACATTTTCGGGCATAGTGCATTATTAGAGATAACATTTCACTA
* *
2302904 AAAAGTTGGTAAAGATGAT
129 AAAAGTTGCTAAAGATGAC
* * * * *
2302923 TGATGAGACACTAAAAAGTTGCTGACATTTTTTGGCATGATGCATTATTAATGACATTTTTTGAA
1 TGATG-GGCACTAAAAAGTTGTTGGCATTTTTTTGCATGATGCATTATTAATGACATTTTATGAA
*
2302988 GATTATTAATGGATCGTTTTGACATTTTC
65 GATTATTAATGGCTCGTTTTGACATTTTC
2303017 AGGTTAAAGC
Statistics
Matches: 209, Mismatches: 30, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
146 2 0.01
147 28 0.13
148 54 0.26
149 125 0.60
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.38
Consensus pattern (147 bp):
TGATGGGCACTAAAAAGTTGTTGGCATTTTTTTGCATGATGCATTATTAATGACATTTTATGAAG
ATTATTAATGGCTCGTTTTGACATTTTCGGGCATAGTGCATTATTAGAGATAACATTTCACTAAA
AAGTTGCTAAAGATGAC
Found at i:2303669 original size:16 final size:17
Alignment explanation
Indices: 2303648--2303681 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
2303638 CTGAGGTGTT
2303648 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
2303664 ACATTGACTTTTACAAA
1 ACATTGACTTTTACAAA
2303681 A
1 A
2303682 GAATGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:2307817 original size:16 final size:17
Alignment explanation
Indices: 2307792--2307825 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2307782 CTGAGATATC
2307792 ACATTAACTTTT-CAAA
1 ACATTAACTTTTACAAA
*
2307808 ACATTTACTTTTACAAA
1 ACATTAACTTTTACAAA
2307825 A
1 A
2307826 GAATGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (17 bp):
ACATTAACTTTTACAAA
Found at i:2312723 original size:4 final size:4
Alignment explanation
Indices: 2312708--2313865 Score: 2242
Period size: 4 Copynumber: 291.2 Consensus size: 4
2312698 TTTTTAAGTC
2312708 TTCA TT-A TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2312755 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2312803 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2312851 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2312899 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2312947 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2312995 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313043 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313091 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313139 TTCA TTCA -TCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313186 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313234 TTCA TTCA TTCA TTCA TTCA TTCA -TCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313281 TTCA TTCA TTCA TTCA TTCA TTCA TTCA -TCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313328 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313376 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313424 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA -TCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313471 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA -TTCA
2313520 TTCA TTCA -TCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313567 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313615 TTCA TTCA TTCA -TCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313662 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313710 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313758 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
2313806 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
*
2313854 -TCA TTTA TTCA T
1 TTCA TTCA TTCA T
2313866 CACCCTCCTC
Statistics
Matches: 1143, Mismatches: 2, Indels: 18
0.98 0.00 0.02
Matches are distributed among these distances:
3 24 0.02
4 1115 0.98
5 4 0.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TTCA
Found at i:2320069 original size:2 final size:2
Alignment explanation
Indices: 2320062--2320140 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
2320052 TATCTCTATT
2320062 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
2320104 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 T
2320141 GTGAGATTGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2323651 original size:35 final size:35
Alignment explanation
Indices: 2323602--2323748 Score: 190
Period size: 35 Copynumber: 4.2 Consensus size: 35
2323592 AGTTTGCATC
* * *
2323602 GATTCAAGTTGAACGGAAGGAAGAATCGCACTTCT
1 GATTCAAGTCGAACGGAAGGAGGCATCGCACTTCT
*
2323637 GATTCAAGTCGAACGGAATGAGGCATCGCACTT-T
1 GATTCAAGTCGAACGGAAGGAGGCATCGCACTTCT
* *
2323671 CGATTCAAGTAGAACGGAAGGAGGCATCGTACTTCT
1 -GATTCAAGTCGAACGGAAGGAGGCATCGCACTTCT
* *
2323707 GATTCAAGTCGAACGAAAGGAGGCATCACACTT-T
1 GATTCAAGTCGAACGGAAGGAGGCATCGCACTTCT
2323741 CGATTCAA
1 -GATTCAA
2323749 CTAGAACAAA
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
34 2 0.02
35 95 0.97
36 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (35 bp):
GATTCAAGTCGAACGGAAGGAGGCATCGCACTTCT
Found at i:2323713 original size:70 final size:70
Alignment explanation
Indices: 2323600--2323755 Score: 240
Period size: 70 Copynumber: 2.2 Consensus size: 70
2323590 AAAGTTTGCA
* * * *
2323600 TCGATTCAAGTTGAACGGAAGGAAGAATCGCACTTCTGATTCAAGTCGAACGGAATGAGGCATCG
1 TCGATTCAAGTAGAACGGAAGGAAGAATCGCACTTCTGATTCAAGTCGAACGAAAGGAGGCATCA
2323665 CACTT
66 CACTT
* * *
2323670 TCGATTCAAGTAGAACGGAAGGAGGCATCGTACTTCTGATTCAAGTCGAACGAAAGGAGGCATCA
1 TCGATTCAAGTAGAACGGAAGGAAGAATCGCACTTCTGATTCAAGTCGAACGAAAGGAGGCATCA
2323735 CACTT
66 CACTT
*
2323740 TCGATTCAACTAGAAC
1 TCGATTCAAGTAGAAC
2323756 AAATGATTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 78 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (70 bp):
TCGATTCAAGTAGAACGGAAGGAAGAATCGCACTTCTGATTCAAGTCGAACGAAAGGAGGCATCA
CACTT
Found at i:2330431 original size:29 final size:29
Alignment explanation
Indices: 2330385--2330487 Score: 190
Period size: 29 Copynumber: 3.6 Consensus size: 29
2330375 TTTCATATGT
*
2330385 TCATGTA-CTTATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
2330413 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
2330442 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
2330471 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
2330488 CTTCACATCA
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
28 7 0.10
29 66 0.90
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:2330520 original size:12 final size:12
Alignment explanation
Indices: 2330503--2330538 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2330493 CATCATGTTC
2330503 TCATATCACATG
1 TCATATCACATG
*
2330515 TCATATCACATA
1 TCATATCACATG
2330527 TCATATCACATG
1 TCATATCACATG
2330539 AACATATATA
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:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:2332549 original size:22 final size:18
Alignment explanation
Indices: 2332506--2332575 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
2332496 TTCAGTATTC
*
2332506 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
2332524 GTCCCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCAC----TAT
*
2332546 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
2332564 GTCCCGAAGGAC
1 GTCCCGAAGGAC
2332576 TACTCCTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 28 0.62
22 17 0.38
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.20
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:2334192 original size:64 final size:62
Alignment explanation
Indices: 2334087--2334243 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 62
2334077 TAATGAAGGT
* * * **
2334087 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATG-TTGTATTATTATAGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATT-TTA-AAAG
* *
2334151 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATGTTTCTATTTTAAAAG
*
2334214 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
2334244 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
63 4 0.05
64 68 0.85
65 8 0.10
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATTTTAAAAG
Found at i:2334304 original size:21 final size:21
Alignment explanation
Indices: 2334278--2334333 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
2334268 TTAACCTTGA
2334278 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
2334299 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
2334320 TGCATCGATGCACT
1 TGCATCGATGCACT
2334334 CTGCCCAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACTATGAATG
Found at i:2337520 original size:18 final size:18
Alignment explanation
Indices: 2337497--2337560 Score: 83
Period size: 18 Copynumber: 3.3 Consensus size: 18
2337487 TTCAGTAGTC
2337497 GTCCCGTAGGACCACTAT
1 GTCCCGTAGGACCACTAT
*
2337515 GTCCCGAAGGACCACTGTATAT
1 GTCCCGTAGGACCAC----TAT
2337537 GTCCCGTAGGACCACTAT
1 GTCCCGTAGGACCACTAT
2337555 GTCCCG
1 GTCCCG
2337561 AATGACTACT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 23 0.57
22 17 0.43
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.22
Consensus pattern (18 bp):
GTCCCGTAGGACCACTAT
Found at i:2339141 original size:64 final size:62
Alignment explanation
Indices: 2339036--2339192 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 62
2339026 TAATGAAGGT
* * * **
2339036 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATG-TTGTATTATTATAGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATT-TTA-AAAG
* *
2339100 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATGTTTCTATTTTAAAAG
*
2339163 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
2339193 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
63 4 0.05
64 68 0.85
65 8 0.10
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATTTTAAAAG
Found at i:2342447 original size:22 final size:18
Alignment explanation
Indices: 2342404--2342473 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
2342394 TTCAGTATTC
*
2342404 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
2342422 GTCCCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCAC----TAT
*
2342444 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
2342462 GTCCCGAAGGAC
1 GTCCCGAAGGAC
2342474 TACTCCTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 28 0.62
22 17 0.38
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.20
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:2344076 original size:64 final size:63
Alignment explanation
Indices: 2343943--2344084 Score: 155
Period size: 64 Copynumber: 2.2 Consensus size: 63
2343933 TAATGAAGGT
* * * * *
2343943 ATGCATCGATGCACTACTGATGCATTGGTGCATAAAATGCATTCGATGTTGTATTATTATAGGG
1 ATGCATCGATGCA-TACTGATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
2344007 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTGATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
2344069 G
63 G
2344070 AGTGCATCGATGCAT
1 A-TGCATCGATGCAT
2344085 TACCAATGCA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 57 0.85
65 7 0.10
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCATACTGATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:2347376 original size:22 final size:18
Alignment explanation
Indices: 2347333--2347402 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
2347323 TTCAGTATTC
*
2347333 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
2347351 GTCCCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCAC----TAT
*
2347373 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
2347391 GTCCCGAAGGAC
1 GTCCCGAAGGAC
2347403 TACTCTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 28 0.62
22 17 0.38
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.20
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:2349020 original size:64 final size:62
Alignment explanation
Indices: 2348915--2349071 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 62
2348905 TAATGAAGGT
* * * **
2348915 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATG-TTGTATTATTATAGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATT-TTA-AAAG
* *
2348979 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATGTTTCTATTTTAAAAG
*
2349042 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
2349072 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
63 4 0.05
64 68 0.85
65 8 0.10
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATTTTAAAAG
Found at i:2352982 original size:33 final size:34
Alignment explanation
Indices: 2352945--2353011 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
2352935 TTTTAGCTGC
*
2352945 AAATTTCATAAAAC-AAAGATCGAATTGAAGAGA
1 AAATTTCATAAAACAAAACATCGAATTGAAGAGA
2352978 AAATTTCATAAAACAAAACATCGAATTGAAGAGA
1 AAATTTCATAAAACAAAACATCGAATTGAAGAGA
2353012 TTGTTGTCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 14 0.44
34 18 0.56
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.21
Consensus pattern (34 bp):
AAATTTCATAAAACAAAACATCGAATTGAAGAGA
Found at i:2359092 original size:527 final size:527
Alignment explanation
Indices: 2358099--2359155 Score: 1855
Period size: 527 Copynumber: 2.0 Consensus size: 527
2358089 TTTGTATTAG
* *
2358099 TTGTCATGTAAAATTATTAGTTGTCATATAACTAATAATAGTTGTATAATGCATAATAATAATTC
1 TTGTCATGCAAAATTATTAGTTGTCATACAACTAATAATAGTTGTATAATGCATAATAATAATTC
* **
2358164 ATAATGCATTGTAAGTTGACAACAATAATGATTCATAGTTGGCACTAATAATGGTTGAAAAGTGG
66 ATAATGCATTGTAAGTTGACAACAATAATGATTCATAGTTGACACTAATAATGGTTGAAAAGTAA
2358229 CATGGCAAAATCTCACATTTAGTCATTGTAATTTAGAGTATTTTCAAAATTAGTCCTTAAAGCTT
131 CATGGCAAAATCTCACATTTAGTCATTGTAATTTAGAGTATTTTCAAAATTAGTCCTTAAAGCTT
* * *
2358294 CTACTATAAATACTCTAGCTCATTTAGCTTCAAAACCATCCCATAGCATTCTATCTTTCTTCCAA
196 CTACTATAAATACCCTAGCTCATTTAGCTTCAAAACCATCCCAAAGCATTCTAGCTTTCTTCCAA
*
2358359 TACTAGAGAGAATTTAGAGAGTTTCTTGAGAGTTGTTTTCTCCTTTTTATCAAGAGAGAATTATC
261 TACTAGAAAGAATTTAGAGAGTTTCTTGAGAGTTGTTTTCTCCTTTTTATCAAGAGAGAATTATC
*
2358424 ATTGTTTTCTCCTTGAGTAGATTGAGAGAAGTTGTAATTTCTATTTTCTCATAGTGAAATTCTTC
326 ATTGTTTTCTCCTTGAGTAGATTGAGAGAAGTTGTAATTCCTATTTTCTCATAGTGAAATTCTTC
* *
2358489 TACCGTTGCCCGTGGTTTTTACCCTATATTATTTAGGGATTTTCTACGTAAATTTTGTGTCTCTT
391 TACCGTTGCCCGTGGTTTTTACCCTATATTATTTAGGGATTTTCCACGTAAATTTTGTGCCTCTT
* * *
2358554 TTATCTTCATTTTTATTTTCTCAAATTATCAGTTGTGATTTTGCTTTATTCGATAGCCGTCTTCC
456 TTATCTTCATTTTTATTTTCTCAAATTATCAATTATGATTTTGCTTTATTCGATAGCCATCTTCC
2358619 GCAACAA
521 GCAACAA
* **
2358626 TTGTCATGCAAAATTATTAGTTGTCATACAACTGATAATAGTTGTATAATGCATAATAATGGTTC
1 TTGTCATGCAAAATTATTAGTTGTCATACAACTAATAATAGTTGTATAATGCATAATAATAATTC
* *
2358691 ATAATGCATTGTAAGTTGGCAACAATAATGGTTCATAGTTGACACTAATAATGGTTGAAAAGTAA
66 ATAATGCATTGTAAGTTGACAACAATAATGATTCATAGTTGACACTAATAATGGTTGAAAAGTAA
* *
2358756 CATGGCAAAATCTCACATTTAGTCATTGTAATTTAGGGTATTTTCAATATTAGTCCTTAAAGCTT
131 CATGGCAAAATCTCACATTTAGTCATTGTAATTTAGAGTATTTTCAAAATTAGTCCTTAAAGCTT
*
2358821 CTACTATAAATACCCTAGCTTATTTAGCTTCAAAACCATCCCAAAGCATTCTAGCTTTCTTCCAA
196 CTACTATAAATACCCTAGCTCATTTAGCTTCAAAACCATCCCAAAGCATTCTAGCTTTCTTCCAA
*
2358886 TACTAGAAAGAATTTAGAGAGTTTCTTGAGAGTTGTTTTCTCTTTTTTTATCAAGAGAGAATTAT
261 TACTAGAAAGAATTTAGAGAGTTTCTTGAGAGTTGTTTTCTC-CTTTTTATCAAGAGAGAATTAT
*
2358951 CATTGTTTTCTCCTTG-GTAGATTGGGAGAAGTTGTAATTCCTATTTTCTCATAGTGAAATTCTT
325 CATTGTTTTCTCCTTGAGTAGATTGAGAGAAGTTGTAATTCCTATTTTCTCATAGTGAAATTCTT
* *
2359015 CTACCGTTGCCCGTGGTTTTTATCCTATATTATTTAGGGGTTTTCCACGTAAATTTTGTGCCTCT
390 CTACCGTTGCCCGTGGTTTTTACCCTATATTATTTAGGGATTTTCCACGTAAATTTTGTGCCTCT
2359080 TTTATCTTCATTTTTATTTTCTCAAATTATCAATTATGATTTTGCTTTATTCGATAGCCATCTTC
455 TTTATCTTCATTTTTATTTTCTCAAATTATCAATTATGATTTTGCTTTATTCGATAGCCATCTTC
2359145 CGCAACAA
520 CGCAACAA
2359153 TTG
1 TTG
2359156 GTATCAGAGT
Statistics
Matches: 502, Mismatches: 27, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
527 465 0.93
528 37 0.07
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (527 bp):
TTGTCATGCAAAATTATTAGTTGTCATACAACTAATAATAGTTGTATAATGCATAATAATAATTC
ATAATGCATTGTAAGTTGACAACAATAATGATTCATAGTTGACACTAATAATGGTTGAAAAGTAA
CATGGCAAAATCTCACATTTAGTCATTGTAATTTAGAGTATTTTCAAAATTAGTCCTTAAAGCTT
CTACTATAAATACCCTAGCTCATTTAGCTTCAAAACCATCCCAAAGCATTCTAGCTTTCTTCCAA
TACTAGAAAGAATTTAGAGAGTTTCTTGAGAGTTGTTTTCTCCTTTTTATCAAGAGAGAATTATC
ATTGTTTTCTCCTTGAGTAGATTGAGAGAAGTTGTAATTCCTATTTTCTCATAGTGAAATTCTTC
TACCGTTGCCCGTGGTTTTTACCCTATATTATTTAGGGATTTTCCACGTAAATTTTGTGCCTCTT
TTATCTTCATTTTTATTTTCTCAAATTATCAATTATGATTTTGCTTTATTCGATAGCCATCTTCC
GCAACAA
Found at i:2367192 original size:31 final size:31
Alignment explanation
Indices: 2367154--2367218 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
2367144 AAGCTTGTAT
2367154 CTAGTTATAATAGAAATGCTTAGGTTGTTAA
1 CTAGTTATAATAGAAATGCTTAGGTTGTTAA
2367185 CTAGTTATAATAGAAATGCTTAGGTTGTTAA
1 CTAGTTATAATAGAAATGCTTAGGTTGTTAA
2367216 CTA
1 CTA
2367219 ATTCTTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (31 bp):
CTAGTTATAATAGAAATGCTTAGGTTGTTAA
Found at i:2369575 original size:4 final size:4
Alignment explanation
Indices: 2369566--2369599 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
2369556 ATCAAAAGAA
* *
2369566 ACAT ACAT ACAT ACAA ACAT AGAT ACAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
2369600 CCAAGAGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.24, G:0.03, T:0.21
Consensus pattern (4 bp):
ACAT
Found at i:2369585 original size:16 final size:16
Alignment explanation
Indices: 2369564--2369596 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2369554 TAATCAAAAG
2369564 AAACATACATACATAC
1 AAACATACATACATAC
*
2369580 AAACATAGATACATAC
1 AAACATACATACATAC
2369596 A
1 A
2369597 TACCCAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.03, T:0.18
Consensus pattern (16 bp):
AAACATACATACATAC
Found at i:2375021 original size:19 final size:20
Alignment explanation
Indices: 2374981--2375022 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
2374971 GCCATTCTAG
*
2374981 AAATCAATTTCCGATAATAT
1 AAATCAATTTACGATAATAT
2375001 AAATC-ATTTACGA-AATCAT
1 AAATCAATTTACGATAAT-AT
2375020 AAA
1 AAA
2375023 ATCGAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 3 0.15
19 12 0.60
20 5 0.25
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (20 bp):
AAATCAATTTACGATAATAT
Found at i:2376719 original size:12 final size:12
Alignment explanation
Indices: 2376702--2376728 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2376692 TTTTTTAATA
2376702 TTTAATTTTATT
1 TTTAATTTTATT
2376714 TTTAATTTTATT
1 TTTAATTTTATT
2376726 TTT
1 TTT
2376729 TAGAAAAATC
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTAATTTTATT
Found at i:2376730 original size:19 final size:19
Alignment explanation
Indices: 2376693--2376727 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2376683 AGATCAAAGT
2376693 TTTTTAATATTTAATTTTA
1 TTTTTAATATTTAATTTTA
2376712 TTTTTAAT-TTT-ATTTT
1 TTTTTAATATTTAATTTT
2376728 TTAGAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTAATATTTAATTTTA
Found at i:2390623 original size:2 final size:2
Alignment explanation
Indices: 2390616--2390655 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2390606 ATAGATATGA
2390616 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
2390656 CCGAGGTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2391929 original size:2 final size:2
Alignment explanation
Indices: 2391922--2391963 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2391912 CTGCTATTTC
2391922 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
2391964 AACACTCACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2395333 original size:29 final size:29
Alignment explanation
Indices: 2395300--2395361 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 29
2395290 GTTAAATGTT
**
2395300 TAACGTTTGTTTTGTTCTAATTTGGTGCC
1 TAACGTTTGTTTCATTCTAATTTGGTGCC
2395329 TAAC----GTTTCATTCTAATTTGGTGCC
1 TAACGTTTGTTTCATTCTAATTTGGTGCC
2395354 TAACGTTT
1 TAACGTTT
2395362 CATTCTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
25 23 0.85
29 4 0.15
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (29 bp):
TAACGTTTGTTTCATTCTAATTTGGTGCC
Found at i:2395336 original size:25 final size:25
Alignment explanation
Indices: 2395314--2395368 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
2395304 GTTTGTTTTG
2395314 TTCTAATTTGGTGCCTAACGTTTCA
1 TTCTAATTTGGTGCCTAACGTTTCA
2395339 TTCTAATTTGGTGCCTAACGTTTCA
1 TTCTAATTTGGTGCCTAACGTTTCA
2395364 TTCTA
1 TTCTA
2395369 TAATTCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (25 bp):
TTCTAATTTGGTGCCTAACGTTTCA
Found at i:2395561 original size:3 final size:3
Alignment explanation
Indices: 2395479--2395550 Score: 126
Period size: 3 Copynumber: 24.0 Consensus size: 3
2395469 TTGGTCACCC
*
2395479 CCT CCT CCT CCT CCT CCT CCT CAT CCT CCT CCT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
*
2395527 CCT CCT CCT CCT CCT CCT CAT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT
2395551 TTTTCTCCTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.03, C:0.64, G:0.00, T:0.33
Consensus pattern (3 bp):
CCT
Found at i:2399512 original size:38 final size:38
Alignment explanation
Indices: 2399435--2399512 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 38
2399425 ATTGAACCTG
* * * *
2399435 ATATATTTTTATATAAATTATGTTGAAGTAAAATTTTA
1 ATATATTTTTAAATAAATTATGTTAAAATAAAATATTA
**
2399473 ATATATTTTTTAAATAAATTATG-TAAAATTTAATATTA
1 ATATA-TTTTTAAATAAATTATGTTAAAATAAAATATTA
2399511 AT
1 AT
2399513 TAAAATAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
38 17 0.52
39 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (38 bp):
ATATATTTTTAAATAAATTATGTTAAAATAAAATATTA
Found at i:2399577 original size:27 final size:27
Alignment explanation
Indices: 2399540--2399597 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
2399530 ATAATAAAAT
*
2399540 AATATATTATCAATGAATTTTTATTTA
1 AATATATTATCAATGAATTTTTATATA
*
2399567 AATATATTATCGATGAATTTTTATATA
1 AATATATTATCAATGAATTTTTATATA
2399594 AATA
1 AATA
2399598 ATTTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (27 bp):
AATATATTATCAATGAATTTTTATATA
Found at i:2399602 original size:15 final size:15
Alignment explanation
Indices: 2399582--2399615 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2399572 ATTATCGATG
2399582 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
2399597 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
2399612 AATT
1 AATT
2399616 AGAATTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:2406644 original size:182 final size:182
Alignment explanation
Indices: 2406351--2406997 Score: 886
Period size: 182 Copynumber: 3.6 Consensus size: 182
2406341 TACAAATGAA
* * * * *
2406351 AAATGTATCGATCTATAGCAATATAACAGGTAAAAATATGATAAAATCA-GTGTC-ATTATAATA
1 AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAA-CAGGTCTCGA-AATGATA
** *
2406414 AAACCGGTAAACCGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATAGACACTTT
64 AAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTT
* * *
2406479 TGTAATTTAAAAGAGAAGAAGTTATAGCGTCTAAAAAGTGTCGATATTTTATAC
129 CGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* * * *
2406533 AAATGTATTGATCCATAGCAATATAACATGTAATAATATTACAAAACAGGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGATAAA
* * * *
2406598 ACCAGTAAAAAGCTACCAGATATATTGAAAATGTCGATACATTAATATAAGTATCGACACTTTCG
66 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTCG
*
2406663 TAATTTAAAAGAGAAGAAGTAATAGCGCCTAAAAAGTGTCGATACTTTATAC
131 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* * * *
2406715 AAATATATCGATCCATAGCAATATAACAAGTAATAATATGACAAAACATGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGATAAA
* *
2406780 ACCGGTAAAAAGATATCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTCG
66 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTCG
* * *
2406845 TAATTTAAAAGAGAAGAAATTATTGTGCCTAAAAAGTGTCGATACTTTATGA-
131 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT-AC
* * * * * *
2406897 AAACGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCGGTATCGAAATGACAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGATAAA
* ** * *
2406962 ACCGATAAAGCGCTACCGGTTATGTTGAAAGTGTCG
66 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCG
2406998 GTACTTTAAT
Statistics
Matches: 410, Mismatches: 52, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
181 2 0.00
182 406 0.99
183 2 0.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGATAAA
ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTCG
TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
Found at i:2407971 original size:19 final size:19
Alignment explanation
Indices: 2407947--2407996 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
2407937 AAATGTAGGG
2407947 TTAATTTTGTATAAGATTT
1 TTAATTTTGTATAAGATTT
* *
2407966 TTAATTTTATATACGATTT
1 TTAATTTTGTATAAGATTT
*
2407985 ATAATTTTGTAT
1 TTAATTTTGTAT
2407997 GTGAATGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:2408777 original size:198 final size:198
Alignment explanation
Indices: 2408272--2409087 Score: 1278
Period size: 198 Copynumber: 4.1 Consensus size: 198
2408262 TTGTCTAAGT
** * *
2408272 ATACTTTGTGTCCAGAATGATTTCCTTACCAA-GTGCATGGA-AATGTGTCGATACCTTAATAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGT-CA-CCATAATGTGTCGATACATTTATAAA
*
2408335 AAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAAC
64 AAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAAC
* * * *
2408400 CGGTCCAAATACACCAGTTTATGAGAAAATAGGTGTACATAAAGTATCGACACATTTTT-AATTT
129 CGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACAC-TTTTTGAATTT
2408464 GTGTCG
193 GTGTCG
* * *
2408470 ATCACATACTTTGTGTCCACAATGATTTCCTTACCAAGGTCAACATAATGTGTCGATACATCTAT
1 -----ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAATGTGTCGATACATTTAT
2408535 AAAAAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
61 AAAAAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
* * *
2408600 AACCGGTCTAATTACACCTGTTTATGAGAAAACATGTGTACATGAAGTATCGACACTTTTTGAAT
126 AACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTGAAT
*
2408665 TTGTGTCT
191 TTGTGTCG
* *
2408673 TTACTTTGTGTCCAGAATGATTTTCTTACCAAGGTCACCATAATGTGTCGATACATTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAATGTGTCGATACATTTATAAAAA
*
2408738 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAAGTAAATTATCAATCTAACCG
66 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
* * * *
2408803 GTCTAATTACACCGGCTTATGAGAAAACAGGTGTACATGAAGTATCAACACTTTTTTAATTTGTG
131 GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTGAATTTGTG
2408868 TCG
196 TCG
*
2408871 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAAGGTGTCGATACATTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAATGTGTCGATACATTTATAAAAA
2408936 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
66 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
* * *
2409001 GTCTAAATACATCGGTTTATGAGAAAACATGTGTACATGAAGTATCGACACTTTTTGAATTTGTA
131 GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTGAATTTGTG
2409066 TCG
196 TCG
* *
2409069 ATACTTTTTGTCCAAAATG
1 ATACTTTGTGTCCAGAATG
2409088 TAAATGGTCA
Statistics
Matches: 571, Mismatches: 39, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
198 390 0.68
202 6 0.01
203 173 0.30
204 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (198 bp):
ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAATGTGTCGATACATTTATAAAAA
GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTGAATTTGTG
TCG
Found at i:2409586 original size:15 final size:15
Alignment explanation
Indices: 2409566--2409617 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
2409556 AGAATCGGAG
*
2409566 CTCTTCTCAACCCAT
1 CTCTTCTCAACCCAA
*
2409581 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAA
2409596 CTCTTCTCAACCCAA
1 CTCTTCTCAACCCAA
2409611 CTCTTCT
1 CTCTTCT
2409618 GAGGAAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.33
Consensus pattern (15 bp):
CTCTTCTCAACCCAA
Found at i:2410114 original size:16 final size:16
Alignment explanation
Indices: 2410093--2410128 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
2410083 TTTATTCGAC
2410093 CTTGTAGCAATAATTT
1 CTTGTAGCAATAATTT
2410109 CTTGTAGCAATAATTT
1 CTTGTAGCAATAATTT
2410125 CTTG
1 CTTG
2410129 GCAGACATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (16 bp):
CTTGTAGCAATAATTT
Found at i:2412289 original size:23 final size:23
Alignment explanation
Indices: 2412263--2412307 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2412253 CACCACAGCT
*
2412263 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
2412286 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2412308 ATATAAGGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:2412511 original size:6 final size:6
Alignment explanation
Indices: 2412500--2413533 Score: 1719
Period size: 6 Copynumber: 177.2 Consensus size: 6
2412490 CCTTAAGAAT
2412500 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2412548 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2412596 CATATA CATATA CATATA C--ATA CATATA CATATA C--ATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2412640 CATATA C--ATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2412686 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2412734 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2412782 CATATA CATATA CATATA CATATA C--ATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2412828 CATATA CATATA C--ATA CATATA CATATA CATAT- -ATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2412872 CATATA CATATA CATATA CATATA CATATA CATAT- -ATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
*
2412918 TATACATA CATATA CATATA CATAT- -ATATA CATATA CATATA CATATA
1 CAT--ATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2412966 CATATA CATATA CATATA C--ATA CATATA CATATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA C--ATATA CATATA CATATA
2413014 CATATA CATATA CATATA CATATA CATATA C--ATA C-TATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2413059 C--ATA CATATA CATATA CATATA CAT-T- -ATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2413102 CATATA CATATA CATATA CATATA CATATA CATATA CATATA C--ATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2413148 CATATA CATATA CATATA CATATA C--ATA -ATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2413193 CATATA CATATA CATATA CATATA CATATA C--ATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2413239 CATATA CATATA CATACATA CATATA CATATA -ATATA C--ATA CATATA
1 CATATA CATATA CAT--ATA CATATA CATATA CATATA CATATA CATATA
*
2413286 CATATA CATATA CATATA CATATA CATATA TATACATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CAT--ATA CATATA CATATA
2413336 CATATA CATATA CATATA CATATA CATATA CATA-A CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2413383 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2413431 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2413479 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
2413527 CATATA C
1 CATATA C
2413534 TAGGGATCAA
Statistics
Matches: 980, Mismatches: 4, Indels: 88
0.91 0.00 0.08
Matches are distributed among these distances:
3 2 0.00
4 60 0.06
5 18 0.02
6 878 0.90
8 22 0.02
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
CATATA
Found at i:2416852 original size:22 final size:21
Alignment explanation
Indices: 2416827--2416872 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2416817 AAAAAAAAGG
*
2416827 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
2416849 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
2416870 TAT
1 TAT
2416873 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:2416981 original size:190 final size:192
Alignment explanation
Indices: 2416547--2417063 Score: 607
Period size: 199 Copynumber: 2.7 Consensus size: 192
2416537 ATCCCAAAAA
* * * *
2416547 CATCGAAACCCGTAACTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGT
1 CATCAAAACCCATAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTAACGGT
* *
2416612 TTTCTGAGAAAATAGGTCTACA-ATATGTATCGACACTTTATTCATTTGTGTCGATACATGTTGT
66 TTTCTGAGAAAATAGGTCTACATA-ATGTATCGACACTTTATACATTTGTGTCGATAC-TTTTGT
** * * * *
2416676 CCAGAATGTATTTCCAAACCAAGTGCACGAACAAAGTGTCGATACATTTATACAAAGTGTCGAT
129 CCAGAATAAATTTCCAAACCAAGTGCACGAACAAAGTGTCGATACATTTAGAAAAAATATCGAT
* * * *
2416740 C-TCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAA
1 CATC--AAA-A-C----C-CATAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAA
* * * * * * *
2416804 TATAACGGTTAT-T-AAAAAAAAGGTATACATAATGTATCGATACTTTATACATTTGTGTCGACA
57 TTTAACGGTTTTCTGAGAAAATAGGTCTACATAATGTATCGACACTTTATACATTTGTGTCGATA
* *
2416867 CTTTATGTCCATAATAAATTTTCCAAA-CAAGTTCACGAA-AAAGTGTCGATACATTTAGAAAAA
122 CTTT-TGTCCAGAATAAA-TTTCCAAACCAAGTGCACGAACAAAGTGTCGATACATTTAGAAAAA
2416930 ATATCGAT
185 ATATCGAT
*
2416938 CATCAAAACCCATAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTATCGGT
1 CATCAAAACCCATAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTAACGGT
* *
2417003 TTTCTGAGAAAATATGTCTACATAATGTATCGACACGTTT-TAAATTTGTGTCGATACTTTT
66 TTTCTGAGAAAATAGGTCTACATAATGTATCGACAC-TTTATACATTTGTGTCGATACTTTT
2417064 TAAAATTACG
Statistics
Matches: 269, Mismatches: 39, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
190 51 0.19
191 3 0.01
192 45 0.17
193 4 0.01
194 2 0.01
195 2 0.01
196 2 0.01
197 3 0.01
198 31 0.12
199 66 0.25
200 11 0.04
201 49 0.18
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (192 bp):
CATCAAAACCCATAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTAACGGT
TTTCTGAGAAAATAGGTCTACATAATGTATCGACACTTTATACATTTGTGTCGATACTTTTGTCC
AGAATAAATTTCCAAACCAAGTGCACGAACAAAGTGTCGATACATTTAGAAAAAATATCGAT
Found at i:2419431 original size:84 final size:86
Alignment explanation
Indices: 2419337--2419495 Score: 250
Period size: 84 Copynumber: 1.9 Consensus size: 86
2419327 AAATAGGTCA
*
2419337 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTA-TGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
2419401 -CGGTTAAATGCCATTTTATT
66 CCAGTTAAATGCCATTTTATT
* * * *
2419421 ATATAAGCGCTGCCTATTACATTTTATAAGCGTTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
2419486 CCAGTTAAAT
66 CCAGTTAAAT
2419496 AATATAACAT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
84 43 0.64
85 16 0.24
86 8 0.12
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (86 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCAGTTAAATGCCATTTTATT
Found at i:2420074 original size:21 final size:23
Alignment explanation
Indices: 2420050--2420095 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
2420040 TTAAATTATT
*
2420050 TAAAAATAAAT-TTAAAATC-GA
1 TAAAAATAAATCTCAAAATCAGA
*
2420071 TAAAAATTAATCTCAAAATCAGA
1 TAAAAATAAATCTCAAAATCAGA
2420094 TA
1 TA
2420096 CAATATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 7 0.33
23 4 0.19
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.28
Consensus pattern (23 bp):
TAAAAATAAATCTCAAAATCAGA
Found at i:2441587 original size:38 final size:38
Alignment explanation
Indices: 2441536--2441612 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2441526 TAAGATCATT
2441536 TCTAAGGTGCTATCGAAAAGGCTTGTCTCTGTTGTTAA
1 TCTAAGGTGCTATCGAAAAGGCTTGTCTCTGTTGTTAA
2441574 TCTAAGGTGCTATCGAAAAGGCTTGTCTCTGTTGTTAA
1 TCTAAGGTGCTATCGAAAAGGCTTGTCTCTGTTGTTAA
2441612 T
1 T
2441613 AGCTTGGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (38 bp):
TCTAAGGTGCTATCGAAAAGGCTTGTCTCTGTTGTTAA
Found at i:2466241 original size:2 final size:2
Alignment explanation
Indices: 2466234--2466258 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2466224 TACTATATCT
2466234 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2466259 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2468870 original size:650 final size:635
Alignment explanation
Indices: 2467838--2469047 Score: 2021
Period size: 650 Copynumber: 1.9 Consensus size: 635
2467828 ACACATAATA
*
2467838 TTAAAAGGGTTAAGGGGTTTTTTTTTTCTTTTCATATATGCGGAGGATGGTTAATTAATAAGTGG
1 TTAAAAGGGATAAGGGG-TTTTTTTTTCTTTTCATATATGCGGAGGATGGTTAATTAATAAGTGG
*
2467903 CTCTCAAGATCTCGGGAAGCCATAGGCATAGCCACGACCTCTTATATGCCTCTCGAGGCGCCGCA
65 CTCTCAAGATCTCGGGAAGCCATAGGCATAGCCACGACCTCTTATATGCCCCTCGAGGCGCCGCA
2467968 TACACTGTATTAATATAATTAATAATTAATTTCTAATTAAGAGCTGCAATTAAGAATACGAGATG
130 TACACTGTATTAATATAATTAATAATTAATTTCTAATTAAGAGCTGCAATTAAGAATACGAGATG
* * * *
2468033 ATGATGATTAGAACTTTAAATAAGATGAGACAGATTACGAGTTACTCGAGATTGATTCGATCAAG
195 ATGATGATTAGAACTTTAAATAAGACGAGACAGATCACGAGTTACTCGAGATTAACTCGATCAAG
* * *
2468098 ATTTGATAAATATTCGGATCGAATGGACTCGACTCGAGTTCTTAACGAGTCGAAACGAACTATTG
260 ACTCGATAAATATTCGGATCGAATGGACTCGACTCGAGTTCTTAACGAGCCGAAACGAACTATTG
* *
2468163 ATATTCAACTCGAAAAGCTCGTGAGCAGCTTGAAAATATAATATATTAAGATTTATTTTTTTAAA
325 ATATTCAACTCGAAAAGCTCGTGAGCAGCTCGAAAATATAATATATTAAGATTTATTTTTTAAAA
*
2468228 AATAAATTATTAATAATATTAACATTTATGTATTGA-TTTTTTTAAATATAAAGTAAGATTTTCA
390 AATAAATTATTAATAATATTAACATTTATGTATTGATTTTTTTTAAATATAAAGTAAGATTTTAA
* *
2468292 TGTATTTAAGGTTCAGGTTCGAGTTTGAGTTTGAGGCTTCAATCGATTTAAGTTTAAGAATTTTT
455 TGTATTTAAGGTTCAGGTTCGAGTTCGAATTTGAGGCTTCAATCGATTTAAGTTTAAGAATTTTT
2468357 TTCATTTCGAGCCTTTTCGAGCTGCTCACGAGCTTCAGTTTAATTCGAGTTTAAAAATTTTAAAC
520 TTCATTTCGAGCCTTTTCGAGCTGCTCACGAGCTTCAGTTTAATTCGAGTTTAAAAATTTTAAAC
2468422 TCGTGAGTTTTCAAGTCGAACTCAATAATACTCGAGCTGAATTTTACTCGT
585 TCGTGAGTTTTCAAGTCGAACTCAATAATACTCGAGCTGAATTTTACTCGT
2468473 TTAAAAGGGATAAGGGG-TTTTTTTTCTTTTCATATATGCGGAGGATGGTTAATTAATAAGTGGC
1 TTAAAAGGGATAAGGGGTTTTTTTTTCTTTTCATATATGCGGAGGATGGTTAATTAATAAGTGGC
2468537 TCTCAAGATCTCGGGAAGCCGTAGCCATAGGCATAGCCACGACCTCTTATATGCCCCTCGAGGCG
66 TCTCAAGATCTCGGG-A-----AGCCATAGGCATAGCCACGACCTCTTATATGCCCCTCGAGGCG
2468602 CCGCATACACTGTGTTAGCCACATATTAATATAATTAATAATTAATTTCTAATTAAGAGCTGCAA
125 CCGCATACAC-----T-G-----TATTAATATAATTAATAATTAATTTCTAATTAAGAGCTGCAA
* ** * *
2468667 TTAAGAATAGGAGATGATGATGATTAGAGTTTTAAATAAGACGAGACAGATCGCGAGTTATTCGA
179 TTAAGAATACGAGATGATGATGATTAGAACTTTAAATAAGACGAGACAGATCACGAGTTACTCGA
2468732 GATTAACTCGATCAAGACTCGATAAATATTC-GATCGAATGGACTCGACTCGAGTTCTTAACGAG
244 GATTAACTCGATCAAGACTCGATAAATATTCGGATCGAATGGACTCGACTCGAGTTCTTAACGAG
*
2468796 CCGAAACGAGCTATTGATATTCAACTCGAAAAGCTCGTGAGCAGCTCGAAAATATAATATATTAA
309 CCGAAACGAACTATTGATATTCAACTCGAAAAGCTCGTGAGCAGCTCGAAAATATAATATATTAA
2468861 GATTTTATTTTTTAAAAAATAAATTATTAATAATATTAACATTTATGTATTGATTTTTTTTAAAT
374 GA-TTTATTTTTTAAAAAATAAATTATTAATAATATTAACATTTATGTATTGATTTTTTTTAAAT
* *
2468926 ATACAGTAAGATTTTAATGTATTTAAGGTTCAGGTTCGAGTTCGAATTTGAGGTTTCAATCGATT
438 ATAAAGTAAGATTTTAATGTATTTAAGGTTCAGGTTCGAGTTCGAATTTGAGGCTTCAATCGATT
*
2468991 TAAGTTTAAGAATTTTTTTCATTTCGAGCTTTTTCGAGCTGCTCACGAGCTTCAGTT
503 TAAGTTTAAGAATTTTTTTCATTTCGAGCCTTTTCGAGCTGCTCACGAGCTTCAGTT
2469048 CAAGATTTCG
Statistics
Matches: 533, Mismatches: 23, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
633 62 0.12
634 1 0.00
635 16 0.03
639 52 0.10
644 1 0.00
645 1 0.00
649 97 0.18
650 176 0.33
651 127 0.24
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (635 bp):
TTAAAAGGGATAAGGGGTTTTTTTTTCTTTTCATATATGCGGAGGATGGTTAATTAATAAGTGGC
TCTCAAGATCTCGGGAAGCCATAGGCATAGCCACGACCTCTTATATGCCCCTCGAGGCGCCGCAT
ACACTGTATTAATATAATTAATAATTAATTTCTAATTAAGAGCTGCAATTAAGAATACGAGATGA
TGATGATTAGAACTTTAAATAAGACGAGACAGATCACGAGTTACTCGAGATTAACTCGATCAAGA
CTCGATAAATATTCGGATCGAATGGACTCGACTCGAGTTCTTAACGAGCCGAAACGAACTATTGA
TATTCAACTCGAAAAGCTCGTGAGCAGCTCGAAAATATAATATATTAAGATTTATTTTTTAAAAA
ATAAATTATTAATAATATTAACATTTATGTATTGATTTTTTTTAAATATAAAGTAAGATTTTAAT
GTATTTAAGGTTCAGGTTCGAGTTCGAATTTGAGGCTTCAATCGATTTAAGTTTAAGAATTTTTT
TCATTTCGAGCCTTTTCGAGCTGCTCACGAGCTTCAGTTTAATTCGAGTTTAAAAATTTTAAACT
CGTGAGTTTTCAAGTCGAACTCAATAATACTCGAGCTGAATTTTACTCGT
Found at i:2471767 original size:23 final size:23
Alignment explanation
Indices: 2471718--2471768 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2471708 ATCTTATATG
* * *
2471718 GCACTTCGGTGCATTTCTACGCG
1 GCACTACGGTGCAATTCTACGCA
* *
2471741 GCACTACGGTGCAATTCTATGTA
1 GCACTACGGTGCAATTCTACGCA
2471764 GCACT
1 GCACT
2471769 TAGGTACATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACGCA
Found at i:2474061 original size:2 final size:2
Alignment explanation
Indices: 2474054--2474107 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
2474044 AAACCAATGA
2474054 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
2474096 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2474108 CAGTATACAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2485692 original size:13 final size:13
Alignment explanation
Indices: 2485674--2485699 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2485664 AACAATTGTT
2485674 CCCTCTTACTCCC
1 CCCTCTTACTCCC
2485687 CCCTCTTACTCCC
1 CCCTCTTACTCCC
2485700 GATCTATTCC
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:0.08, C:0.62, G:0.00, T:0.31
Consensus pattern (13 bp):
CCCTCTTACTCCC
Found at i:2489765 original size:12 final size:13
Alignment explanation
Indices: 2489748--2489776 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2489738 TACTAATTGG
2489748 AAAATA-TTAAAT
1 AAAATATTTAAAT
2489760 AAAATATTTAAAT
1 AAAATATTTAAAT
2489773 AAAA
1 AAAA
2489777 AATCGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATATTTAAAT
Found at i:2491018 original size:52 final size:52
Alignment explanation
Indices: 2490943--2491044 Score: 186
Period size: 52 Copynumber: 2.0 Consensus size: 52
2490933 TCGGTAAAAG
2490943 TATATATACAAAAGTATATATTTGGCCATCTTACCTCAGGATTCTAGTAATA
1 TATATATACAAAAGTATATATTTGGCCATCTTACCTCAGGATTCTAGTAATA
* *
2490995 TATATATACAAAAGTATATATTTGGTCATCTTATCTCAGGATTCTAGTAA
1 TATATATACAAAAGTATATATTTGGCCATCTTACCTCAGGATTCTAGTAA
2491045 GTGTGATAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (52 bp):
TATATATACAAAAGTATATATTTGGCCATCTTACCTCAGGATTCTAGTAATA
Done.