Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000480.1 Hibiscus syriacus cultivar Beakdansim tig00000910_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: 869251
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:143086 original size:6 final size:6
Alignment explanation
Indices: 143041--143070 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
143031 ATGAACAGTG
*
143041 AATGGT AATGAT AATGAT AATGAT AATGAT
1 AATGAT AATGAT AATGAT AATGAT AATGAT
143071 GTTGTTGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (6 bp):
AATGAT
Found at i:148714 original size:15 final size:16
Alignment explanation
Indices: 148696--148729 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
148686 TTTTTTGTTT
148696 AAAATAAAATA-ATGA
1 AAAATAAAATATATGA
*
148711 AAAATAACATATATGA
1 AAAATAAAATATATGA
148727 AAA
1 AAA
148730 TTTTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAATAAAATATATGA
Found at i:148852 original size:2 final size:2
Alignment explanation
Indices: 148845--148892 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
148835 GTTAGTGTAA
148845 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
148887 AT AT AT
1 AT AT AT
148893 GTTACAGACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:152758 original size:22 final size:22
Alignment explanation
Indices: 152712--152773 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
152702 CTTAAAGAGT
* * *
152712 GGTCATTCGGCACATATACAGA
1 GGTCATTCGGGACAAATTCAGA
*
152734 GGTCATTCGGGACAAATTCATA
1 GGTCATTCGGGACAAATTCAGA
* *
152756 GGTCCTTCGGGATAAATT
1 GGTCATTCGGGACAAATT
152774 TCACATGCCC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (22 bp):
GGTCATTCGGGACAAATTCAGA
Found at i:161679 original size:22 final size:22
Alignment explanation
Indices: 161646--161751 Score: 95
Period size: 22 Copynumber: 4.8 Consensus size: 22
161636 CAGAACCTCC
*
161646 AGGGGGAGTCGGTTCCCCTACA
1 AGGGGGAATCGGTTCCCCTACA
* * *
161668 GGGGGGAATCGGTTACCATACA
1 AGGGGGAATCGGTTCCCCTACA
* * *
161690 GGGGGGAATCGATTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTAC-A
* * *
161713 AGGAGGAATCGGTTCCTCTTCA
1 AGGGGGAATCGGTTCCCCTACA
* *
161735 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
161752 TCTGCACCAA
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
22 49 0.73
23 18 0.27
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.22
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTACA
Found at i:161753 original size:23 final size:24
Alignment explanation
Indices: 161691--161754 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
161681 TACCATACAG
161691 GGGGGAATCGATTCCC-CTTCAAA
1 GGGGGAATCGATTCCCTCTTCAAA
* *
161714 GGAGGAATCGGTT-CCTCTTC-AA
1 GGGGGAATCGATTCCCTCTTCAAA
*
161736 GGGGGTATCGATTCCCTCT
1 GGGGGAATCGATTCCCTCT
161755 GCACCAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (24 bp):
GGGGGAATCGATTCCCTCTTCAAA
Found at i:165531 original size:21 final size:21
Alignment explanation
Indices: 165505--165544 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
165495 GAGATTATTT
165505 TCATTTTTCA-ATTTTGAAATA
1 TCATTTTT-ATATTTTGAAATA
165526 TCATTTTTATATTTTGAAA
1 TCATTTTTATATTTTGAAA
165545 AGAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTATATTTTGAAATA
Found at i:169373 original size:22 final size:22
Alignment explanation
Indices: 169319--169380 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
169309 CTTAAAGAGT
* * *
169319 GGTCCTTCGGCACATATACAGA
1 GGTCCTTCGGGACAAATTCAGA
* *
169341 GGTCATTCGGGACAAATTCATA
1 GGTCCTTCGGGACAAATTCAGA
*
169363 GGTCCTTCGGGATAAATT
1 GGTCCTTCGGGACAAATT
169381 TCACATGCTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (22 bp):
GGTCCTTCGGGACAAATTCAGA
Found at i:171634 original size:44 final size:43
Alignment explanation
Indices: 171586--171856 Score: 151
Period size: 44 Copynumber: 6.2 Consensus size: 43
171576 AGGCGTTTAA
171586 TTTTTTCAATCTCACTCTCTACATTT-TCAATTAAGGCCTCTAAG
1 TTTTTTCAATCTCACTCTCTACATTTAT-AATTAAGGCC-CTAAG
* * * * *
171630 TTTTTTCAATCTCAATTTCTACATTTATAATTGAGGCCCTTAT
1 TTTTTTCAATCTCACTCTCTACATTTATAATTAAGGCCCTAAG
* * * ** *
171673 TTTTTTAAATCTCACTTTTTTA-ACTTTATAATTGTGGCCCTTAAA
1 TTTTTTCAATCTCAC-TCTCTACA-TTTATAATTAAGGCCC-TAAG
* * * * * *
171718 TTTTTTTAATCTCACTTTCTA-ACTTTCTAACTGAGTCCCCTAA-
1 TTTTTTCAATCTCACTCTCTACA-TTTATAATTAAG-GCCCTAAG
** * * * * * *
171761 AATTTTCGATCTCAAT-TATACCTTTATAATTGAGGTCCCT-AT
1 TTTTTTCAATCTCACTCTCTACATTTATAATTAAGG-CCCTAAG
* * *
171803 TTTTTTCAATCTCAATTTCTACCTTTATAATTAAGGCCTCTAA-
1 TTTTTTCAATCTCACTCTCTACATTTATAATTAAGGCC-CTAAG
171846 TTTTTTACAAT
1 TTTTTT-CAAT
171857 TTCATAAAAT
Statistics
Matches: 183, Mismatches: 32, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
41 1 0.01
42 32 0.17
43 53 0.29
44 77 0.42
45 20 0.11
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.47
Consensus pattern (43 bp):
TTTTTTCAATCTCACTCTCTACATTTATAATTAAGGCCCTAAG
Found at i:171850 original size:43 final size:43
Alignment explanation
Indices: 171476--171856 Score: 285
Period size: 43 Copynumber: 8.8 Consensus size: 43
171466 TATTATTCAA
* *** *
171476 TCTAACTTTATAATTGAAATCTCTAATTTTTTTCAATC-CATTT
1 TCTACCTTTATAATTGAGGCCTCTAA-TTTTTTCAATCTCAATT
* * * *
171519 TTTACCTTTATAATTGAGGCCCCT-ATTTTTGT-AATTTCACTT
1 TCTACCTTTATAATTGAGGCCTCTAATTTTT-TCAATCTCAATT
* * * * *
171561 T-TAACTTTATAATTGAGGCGTTTAATTTTTTCAATCTCACTC
1 TCTACCTTTATAATTGAGGCCTCTAATTTTTTCAATCTCAATT
* *
171603 TCTACATTT-TCAATTAAGGCCTCTAAGTTTTTTCAATCTCAATT
1 TCTACCTTTAT-AATTGAGGCCTCTAA-TTTTTTCAATCTCAATT
* * * *
171647 TCTACATTTATAATTGAGGCC-CTTATTTTTTTAAATCTCACTTT
1 TCTACCTTTATAATTGAGGCCTC-TAATTTTTTCAATCTCA-ATT
* * * * *
171691 TTTAACTTTATAATTGTGGCC-CTTAAATTTTTTTAATCTCACTT
1 TCTACCTTTATAATTGAGGCCTC-T-AATTTTTTCAATCTCAATT
* * * * * ** *
171735 TCTAACTTTCTAACTGAGTCCCCTAAAATTTTCGATCTCAA-T
1 TCTACCTTTATAATTGAGGCCTCTAATTTTTTCAATCTCAATT
* *
171777 TATACCTTTATAATTGAGGTCC-CTATTTTTTTCAATCTCAATT
1 TCTACCTTTATAATTGAGG-CCTCTAATTTTTTCAATCTCAATT
*
171820 TCTACCTTTATAATTAAGGCCTCTAATTTTTTACAAT
1 TCTACCTTTATAATTGAGGCCTCTAATTTTTT-CAAT
171857 TTCATAAAAT
Statistics
Matches: 268, Mismatches: 54, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
41 27 0.10
42 55 0.21
43 90 0.34
44 80 0.30
45 16 0.06
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.48
Consensus pattern (43 bp):
TCTACCTTTATAATTGAGGCCTCTAATTTTTTCAATCTCAATT
Found at i:171924 original size:16 final size:16
Alignment explanation
Indices: 171903--171938 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
171893 CTCTCTCGTT
171903 AATTCATTTAATTTTG
1 AATTCATTTAATTTTG
*
171919 AATTCATTTAGTTTTG
1 AATTCATTTAATTTTG
171935 AATT
1 AATT
171939 AAATCTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (16 bp):
AATTCATTTAATTTTG
Found at i:174742 original size:27 final size:28
Alignment explanation
Indices: 174695--174755 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
174685 GACTATTACG
174695 TTATTATTAAATACATAAATAATATTAT
1 TTATTATTAAATACATAAATAATATTAT
*
174723 TTATTATT-AATA-ATTTAATAATATTAT
1 TTATTATTAAATACA-TAAATAATATTAT
174750 TT-TTAT
1 TTATTAT
174756 GACATTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 5 0.16
27 18 0.58
28 8 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
TTATTATTAAATACATAAATAATATTAT
Found at i:177733 original size:17 final size:18
Alignment explanation
Indices: 177691--177734 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
177681 CCAATACAAT
177691 AGGAAAAAACAAACTTCA
1 AGGAAAAAACAAACTTCA
*
177709 AGGAAAAAATAAACTTCA
1 AGGAAAAAACAAACTTCA
177727 AGGAAAAA
1 AGGAAAAA
177735 GAGTCGGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.64, C:0.11, G:0.14, T:0.11
Consensus pattern (18 bp):
AGGAAAAAACAAACTTCA
Found at i:185531 original size:20 final size:21
Alignment explanation
Indices: 185506--185545 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
185496 CTCTGTATAG
185506 TAGTATCAATACCAT-AGGCA
1 TAGTATCAATACCATCAGGCA
*
185526 TAGTATCGATACCATCAGGC
1 TAGTATCAATACCATCAGGC
185546 CCCAACTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (21 bp):
TAGTATCAATACCATCAGGCA
Found at i:188576 original size:29 final size:29
Alignment explanation
Indices: 188498--188608 Score: 163
Period size: 29 Copynumber: 3.9 Consensus size: 29
188488 TTTTTTATAA
*
188498 TAATTAACTTGATTTTATAATAATTTA-T
1 TAATTAACTTGATTTTATAATAATTAACT
** *
188526 GGA-TATATTTGATTTTATAATAATTAACT
1 TAATTA-ACTTGATTTTATAATAATTAACT
188555 TAATTAACTTGATTTTATAATAATTAACT
1 TAATTAACTTGATTTTATAATAATTAACT
188584 TAATTAACTTGATTTTATAATAATT
1 TAATTAACTTGATTTTATAATAATT
188609 TATGTATAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
27 2 0.03
28 20 0.27
29 49 0.67
30 2 0.03
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (29 bp):
TAATTAACTTGATTTTATAATAATTAACT
Found at i:188627 original size:34 final size:33
Alignment explanation
Indices: 188497--188649 Score: 147
Period size: 29 Copynumber: 5.0 Consensus size: 33
188487 TTTTTTTATA
*
188497 ATAATTAACTTGATTTTATAATAATTTATGGAT
1 ATAATTAACTTGATTTTATAATAATTTATGTAT
188530 AT-A-T---TTGATTTTATAATAA-TTA---ACT
1 ATAATTAACTTGATTTTATAATAATTTATGTA-T
188555 -TAATTAACTTGATTTTATAATAA-TTA---ACT
1 ATAATTAACTTGATTTTATAATAATTTATGTA-T
188584 -TAATTAACTTGATTTTATAATAATTTATGTAT
1 ATAATTAACTTGATTTTATAATAATTTATGTAT
* *
188616 AATAATTAACTTTATTTTATAATCATTTATGTAT
1 -ATAATTAACTTGATTTTATAATAATTTATGTAT
188650 TTTTTTTGTA
Statistics
Matches: 106, Mismatches: 2, Indels: 23
0.81 0.02 0.18
Matches are distributed among these distances:
24 2 0.02
25 2 0.02
26 1 0.01
27 3 0.03
28 15 0.14
29 44 0.42
30 3 0.03
31 1 0.01
32 2 0.02
33 3 0.03
34 30 0.28
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (33 bp):
ATAATTAACTTGATTTTATAATAATTTATGTAT
Found at i:188661 original size:23 final size:22
Alignment explanation
Indices: 188630--188675 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
188620 ATTAACTTTA
*
188630 TTTTATAATCATTTATGTATTTT
1 TTTTATAATAATTTATGT-TTTT
*
188653 TTTTGTAATAATTTATGTTTTT
1 TTTTATAATAATTTATGTTTTT
188675 T
1 T
188676 AAGTTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (22 bp):
TTTTATAATAATTTATGTTTTT
Found at i:191699 original size:18 final size:17
Alignment explanation
Indices: 191676--191711 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
191666 TATTATCTTA
*
191676 TTAATTCAATTTTTAATT
1 TTAATTCAA-ATTTAATT
191694 TTAATTCAAATTTAATT
1 TTAATTCAAATTTAATT
191711 T
1 T
191712 ATTCTGACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAATTCAAATTTAATT
Found at i:192331 original size:21 final size:21
Alignment explanation
Indices: 192296--192346 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
192286 TTATTGTGTC
* *
192296 AGTTACAAGATTAATTACAAG
1 AGTTACAAAAATAATTACAAG
* *
192317 AGTTGCAAAAATAATTGCAAG
1 AGTTACAAAAATAATTACAAG
192338 AGTTACAAA
1 AGTTACAAA
192347 CGGATGTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (21 bp):
AGTTACAAAAATAATTACAAG
Found at i:195505 original size:15 final size:15
Alignment explanation
Indices: 195485--195518 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
195475 GCCTACCTCA
*
195485 TTCTTCTTTTCTTTC
1 TTCTTCTTTTCCTTC
195500 TTCTTCTTTTCCTTC
1 TTCTTCTTTTCCTTC
195515 TTCT
1 TTCT
195519 CTTCATCATC
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:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TTCTTCTTTTCCTTC
Found at i:196594 original size:18 final size:17
Alignment explanation
Indices: 196540--196588 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
196530 TTGGACCCTT
* *
196540 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
196558 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
196576 AGTGCATTCGATG
1 AGTGCA-TCGATG
196589 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:196758 original size:65 final size:64
Alignment explanation
Indices: 196560--196769 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
196550 TGCACTAAGA
* * ** *
196560 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
* * * *
196624 GTGCATCGATGCATCAAATACATTCGTTGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
**
196687 AA
63 TG
* *
196689 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
196753 G
64 G
*
196754 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
196770 CTCTGAAAAT
Statistics
Matches: 117, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 48 0.41
65 61 0.52
67 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:198887 original size:13 final size:13
Alignment explanation
Indices: 198859--198897 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
198849 TGGGCAATGT
*
198859 TTTGAAAA-ACTA
1 TTTGAAAATAATA
198871 TTTGAAAATAATA
1 TTTGAAAATAATA
*
198884 TTTGTAAATAATA
1 TTTGAAAATAATA
198897 T
1 T
198898 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:203302 original size:21 final size:22
Alignment explanation
Indices: 203276--203318 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
203266 AAGACTATTT
203276 TCATTTTTCAATTTT-GAAATA
1 TCATTTTTCAATTTTGGAAATA
**
203297 TCATTTTTGTATTTTGGAAATA
1 TCATTTTTCAATTTTGGAAATA
203319 GAGTCTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.53
Consensus pattern (22 bp):
TCATTTTTCAATTTTGGAAATA
Found at i:205266 original size:17 final size:18
Alignment explanation
Indices: 205227--205274 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
205217 TTGGACCCTT
*
205227 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCACTAA
*
205245 AGTGCATCGATGCA-TCA
1 AGTGCATCGATGCACTAA
205262 AGTGCATTCGATG
1 AGTGCA-TCGATG
205275 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (18 bp):
AGTGCATCGATGCACTAA
Found at i:205363 original size:57 final size:56
Alignment explanation
Indices: 205255--205363 Score: 139
Period size: 57 Copynumber: 1.9 Consensus size: 56
205245 AGTGCATCGA
* *
205255 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
* * * *
205311 TGCATCAAATGCATTTGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG
1 TGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGG
205364 TAAGTGCATC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
56 18 0.40
57 24 0.53
58 3 0.07
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (56 bp):
TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
Found at i:207751 original size:21 final size:21
Alignment explanation
Indices: 207727--207778 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 21
207717 AGTTTACAAT
207727 CATTCAAGTAATGTAGTTCAA
1 CATTCAAGTAATGTAGTTCAA
*
207748 CATTTAAGGTAATGTAGTTCAA
1 CATTCAA-GTAATGTAGTTCAA
207770 CATTCAAGT
1 CATTCAAGT
207779 GAAATGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (21 bp):
CATTCAAGTAATGTAGTTCAA
Found at i:217204 original size:20 final size:20
Alignment explanation
Indices: 217181--217344 Score: 156
Period size: 20 Copynumber: 8.2 Consensus size: 20
217171 GTTTCTAGAT
* *
217181 TCGCAGCGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
217201 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
*
217221 TCGCAACGCGATAAT-A-TAA
1 TCGCAACGCGATTATGACT-A
*
217240 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
*
217260 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
*
217281 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
* * *
217301 TCGCAACACTATTCTGACTA
1 TCGCAACGCGATTATGACTA
217321 TCGCAACGCGATTATGACTA
1 TCGCAACGCGATTATGACTA
217341 TCGC
1 TCGC
217345 GTTGCGATAA
Statistics
Matches: 117, Mismatches: 20, Indels: 14
0.77 0.13 0.09
Matches are distributed among these distances:
18 1 0.01
19 16 0.14
20 81 0.69
21 17 0.15
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:217293 original size:41 final size:41
Alignment explanation
Indices: 217220--217367 Score: 178
Period size: 41 Copynumber: 3.7 Consensus size: 41
217210 GAATATGTAA
217220 ATCGCAACGCGATAAT--ATAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
217259 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
* * ** *
217300 ATCGCAACACTATTCTGAC-T-ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATAAT-ACATAATCGCAACGCGATTCTGACT
*** *
217340 ATCGCGTTGCGATAATACAAAATCGCAA
1 ATCGCAACGCGATAATACATAATCGCAA
217368 TGCAATTTTC
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
39 18 0.20
40 28 0.31
41 43 0.47
42 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (41 bp):
ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
Found at i:217989 original size:20 final size:20
Alignment explanation
Indices: 217936--217983 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
217926 ATCTCGTTGT
217936 GATAGTCAAATTCGCTTTGC
1 GATAGTCAAATTCGCTTTGC
217956 GATAGTCAAATTCGCTTTGC
1 GATAGTCAAATTCGCTTTGC
217976 GATAGTCA
1 GATAGTCA
217984 TTTTCGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
GATAGTCAAATTCGCTTTGC
Found at i:218019 original size:20 final size:20
Alignment explanation
Indices: 217981--218021 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
217971 TTTGCGATAG
*
217981 TCATTTTCGTGTTATGATTT
1 TCATTTTCGTGTTACGATTT
*
218001 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTACGATTT
218021 T
1 T
218022 AAGTTTCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (20 bp):
TCATTTTCGTGTTACGATTT
Found at i:218028 original size:20 final size:20
Alignment explanation
Indices: 217985--218028 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
217975 CGATAGTCAT
* * *
217985 TTTCGTGTTATGATTTTCAT
1 TTTCGTGTTACGATTTTAAG
*
218005 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTACGATTTTAAG
218025 TTTC
1 TTTC
218029 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTACGATTTTAAG
Found at i:220016 original size:20 final size:20
Alignment explanation
Indices: 219993--220030 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
219983 AATCGCAACG
219993 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAATGCGAAAA
220013 TGAAAATCGCAATGCGAA
1 TGAAAATCGCAATGCGAA
220031 TTTAGTTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (20 bp):
TGAAAATCGCAATGCGAAAA
Found at i:220131 original size:20 final size:20
Alignment explanation
Indices: 220106--220174 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
220096 GCGATTATCC
*
220106 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
*
220126 CGTTGCGATAGT-TATTTCCG
1 CGTTGCGATAGTCAATTT-CG
*
220146 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
220166 CGTTGCGAT
1 CGTTGCGAT
220175 TTTAAGTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:220302 original size:21 final size:20
Alignment explanation
Indices: 220274--220377 Score: 100
Period size: 21 Copynumber: 5.0 Consensus size: 20
220264 GACTCATCTG
*
220274 TCATCGTTCAAGAGGCCTCT
1 TCATCGTTCAAGAGGCCCCT
220294 TCTATCGTTCAAGAGGCCCCT
1 TC-ATCGTTCAAGAGGCCCCT
** *
220315 ATCATCCCTCAAGAGTCCCCT
1 -TCATCGTTCAAGAGGCCCCT
*
220336 CCCATCGTTCAAGAGGCCCCT
1 -TCATCGTTCAAGAGGCCCCT
* * *
220357 GTCATCATTGAAGAGGTCCCT
1 -TCATCGTTCAAGAGGCCCCT
220378 CCCACCATTC
Statistics
Matches: 68, Mismatches: 14, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.26
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCCT
Found at i:220371 original size:42 final size:42
Alignment explanation
Indices: 220297--220392 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
220287 GGCCTCTTCT
*
220297 ATCGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCC
1 ATCGTTCAAGAGGCCCCTATCATCACTCAAGAGGT-CCCTCCC
* * *
220339 ATCGTTCAAGAGGCCCCTGTCATCATTGAAGAGGTCCCTCCC
1 ATCGTTCAAGAGGCCCCTATCATCACTCAAGAGGTCCCTCCC
* *
220381 ACCATTCAAGAG
1 ATCGTTCAAGAG
220393 CCCGATTCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 45 0.96
43 2 0.04
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (42 bp):
ATCGTTCAAGAGGCCCCTATCATCACTCAAGAGGTCCCTCCC
Found at i:221797 original size:14 final size:14
Alignment explanation
Indices: 221774--221826 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
221764 GCTTGTTTAA
*
221774 TTGATTTGTAAAAG
1 TTGATGTGTAAAAG
221788 TTGATGTGTAAAAG
1 TTGATGTGTAAAAG
* **
221802 TTGATTTGTTTAA-
1 TTGATGTGTAAAAG
221815 TTGATGTGTAAA
1 TTGATGTGTAAA
221827 TAATTCTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 9 0.28
14 23 0.72
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (14 bp):
TTGATGTGTAAAAG
Found at i:221823 original size:27 final size:28
Alignment explanation
Indices: 221774--221826 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
221764 GCTTGTTTAA
221774 TTGATTTGTAAAAGTTGATGTGTAAAAG
1 TTGATTTGTAAAAGTTGATGTGTAAAAG
**
221802 TTGATTTGTTTAA-TTGATGTGTAAA
1 TTGATTTGTAAAAGTTGATGTGTAAA
221827 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (28 bp):
TTGATTTGTAAAAGTTGATGTGTAAAAG
Found at i:221969 original size:20 final size:20
Alignment explanation
Indices: 221930--222005 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
221920 AGGTACACTT
* *
221930 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGTCAAAA
* *
221950 TCGTAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
*
221970 TCGCAACGTGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
221990 TCGCAACGCGAAAGTC
1 TCGCAACGCGAAAGTC
222006 CATTCACGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAA
Found at i:222075 original size:20 final size:20
Alignment explanation
Indices: 222047--222225 Score: 87
Period size: 20 Copynumber: 9.6 Consensus size: 20
222037 TTCTCGTTGC
222047 GATAGTCAAATTC-CAGTTAT
1 GATAGTCAAATTCGC-GTTAT
* *
222067 GATAATCAAATTCGCGTTGT
1 GATAGTCAAATTCGCGTTAT
**
222087 GATAGTCAAATTCGCGTTGC
1 GATAGTCAAATTCGCGTTAT
**
222107 GAT-GT----TT-GCGTTGC
1 GATAGTCAAATTCGCGTTAT
* **
222121 GATAGTCATATTCGCGTTGC
1 GATAGTCAAATTCGCGTTAT
**
222141 GATAGTCAAATTCGCGTTGC
1 GATAGTCAAATTCGCGTTAT
* **
222161 GAT--T----TTTGCGTTGC
1 GATAGTCAAATTCGCGTTAT
* **
222175 GATAGTCAAATTCGTGTTGC
1 GATAGTCAAATTCGCGTTAT
*
222195 GATAGTCAAATTCGCGTTGT
1 GATAGTCAAATTCGCGTTAT
*
222215 GATATTCAAAT
1 GATAGTCAAAT
222226 GAATGTGTAA
Statistics
Matches: 135, Mismatches: 11, Indels: 26
0.78 0.06 0.15
Matches are distributed among these distances:
14 22 0.16
15 4 0.03
16 1 0.01
18 1 0.01
19 4 0.03
20 102 0.76
21 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (20 bp):
GATAGTCAAATTCGCGTTAT
Found at i:222119 original size:74 final size:74
Alignment explanation
Indices: 222013--222159 Score: 190
Period size: 74 Copynumber: 2.0 Consensus size: 74
222003 GTCCATTCAC
* * * *
222013 GATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATTC-CAGTTATGATAATCAAA
1 GATAGTCAAATACGCGTTGCGATTTTCGCGTTGCGATAGTCAAATTCGC-GTTACGATAATCAAA
222077 TTCGCGTTGT
65 TTCGCGTTGT
* * * *
222087 GATAGTCAAATTCGCGTTGCGATGTTT-GCGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAA
1 GATAGTCAAATACGCGTTGCGAT-TTTCGCGTTGCGATAGTCAAATTCGCGTTACGATAATCAAA
222151 TTCGCGTTG
65 TTCGCGTTG
222160 CGATTTTTGC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
74 59 0.94
75 4 0.06
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (74 bp):
GATAGTCAAATACGCGTTGCGATTTTCGCGTTGCGATAGTCAAATTCGCGTTACGATAATCAAAT
TCGCGTTGT
Found at i:222158 original size:54 final size:54
Alignment explanation
Indices: 222067--222213 Score: 249
Period size: 54 Copynumber: 2.7 Consensus size: 54
222057 TTCCAGTTAT
* *
222067 GATAATCAAATTCGCGTTGTGATAGTCAAATTCGCGTTGCGATGTTTGCGTTGC
1 GATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATGTTTGCGTTGC
* *
222121 GATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGC
1 GATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATGTTTGCGTTGC
*
222175 GATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTG
1 GATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
222214 TGATATTCAA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 87 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (54 bp):
GATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATGTTTGCGTTGC
Found at i:222448 original size:140 final size:140
Alignment explanation
Indices: 222196--222478 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
222186 TCGTGTTGCG
* *
222196 ATAGTCAAATTCGCGTTGTGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGTGATAATCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
222261 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
222326 AATACACATA
131 AATACACATA
222336 ATAGTCAAATTCGCGTTGTGATAATCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGTGATAATCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
222401 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAATTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
222466 AATACACATA
131 AATACACATA
222476 ATA
1 ATA
222479 CAACGTTTTC
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGTGATAATCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:224617 original size:14 final size:14
Alignment explanation
Indices: 224598--224634 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
224588 ACCCGTGGCA
224598 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
224612 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
224626 TTCTTCTTC
1 TT-TTCTTC
224635 TTTTTCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:224848 original size:24 final size:24
Alignment explanation
Indices: 224821--224874 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
224811 TTGAAACATC
224821 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
224845 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
224869 ATCAAA
1 ATCAAA
224875 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:224888 original size:24 final size:24
Alignment explanation
Indices: 224821--224888 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
224811 TTGAAACATC
* * *
224821 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
224845 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
224869 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
224889 TAGTACTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:225720 original size:20 final size:20
Alignment explanation
Indices: 225695--225843 Score: 88
Period size: 20 Copynumber: 7.3 Consensus size: 20
225685 GAAATTCAGT
*
225695 GTTGCGACAGTCAGAATTGC
1 GTTGCGACAGTCAGAATCGC
* *
225715 GTTGCGATAGTTAGAATCGC
1 GTTGCGACAGTCAGAATCGC
*
225735 GTTGCGATCA-TCAGAATCGA
1 GTTGCGA-CAGTCAGAATCGC
** * * *
225755 GTTGCGA-TTTTATATTATCGT
1 GTTGCGACAGTCAGA--ATCGC
* **
225776 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-CA-GTCAGAATCGC
*
225797 GTTGCGATAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
* * *
225817 GTTGCGATAGTTAAAATCGC
1 GTTGCGACAGTCAGAATCGC
225837 GTTGCGA
1 GTTGCGA
225844 ATCTGGAAAC
Statistics
Matches: 103, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
19 5 0.05
20 72 0.70
21 23 0.22
23 2 0.02
24 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (20 bp):
GTTGCGACAGTCAGAATCGC
Found at i:225779 original size:21 final size:21
Alignment explanation
Indices: 225750--225804 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
225740 GATCATCAGA
*
225750 ATCGAGTTGCGATTTTATATT
1 ATCGAGTTGCGATTATATATT
* *
225771 ATCGTGTTGCGATTATGTATT
1 ATCGAGTTGCGATTATATATT
*
225792 ATCGCGTTGCGAT
1 ATCGAGTTGCGAT
225805 AGTCAGAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.44
Consensus pattern (21 bp):
ATCGAGTTGCGATTATATATT
Found at i:229441 original size:18 final size:18
Alignment explanation
Indices: 229418--229459 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
229408 TGTCTTGTTG
*
229418 GTGGAGATAGTGTTTGTA
1 GTGGAGATAGTGCTTGTA
229436 GTGGAGATAGTGCTTGTA
1 GTGGAGATAGTGCTTGTA
229454 GTGGAG
1 GTGGAG
229460 CATGGTGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.02, G:0.43, T:0.33
Consensus pattern (18 bp):
GTGGAGATAGTGCTTGTA
Found at i:229759 original size:47 final size:49
Alignment explanation
Indices: 229706--229813 Score: 136
Period size: 49 Copynumber: 2.2 Consensus size: 49
229696 ATGGAATATA
*
229706 AATATCAAATCTTG-A-AGGAGAGA-TCTGTT-CTGCTT-CTTTCTAAAGGG
1 AATATCAAATCTCGAAGAGGAGAGACT-TGTTCCTGCTTAC--TCTAAAGGG
*
229753 AATATCAAATCTCGAAGAGGAGAGACTTGTTCCTGCTTACTCTGAAGGG
1 AATATCAAATCTCGAAGAGGAGAGACTTGTTCCTGCTTACTCTAAAGGG
229802 AATATCAAATCT
1 AATATCAAATCT
229814 GGGGGAGTTG
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
47 13 0.24
48 1 0.02
49 32 0.59
50 7 0.13
51 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (49 bp):
AATATCAAATCTCGAAGAGGAGAGACTTGTTCCTGCTTACTCTAAAGGG
Found at i:229917 original size:48 final size:48
Alignment explanation
Indices: 229846--230217 Score: 550
Period size: 48 Copynumber: 7.8 Consensus size: 48
229836 GGGGCAGATT
* * * *
229846 TGTTCCACTTACTCTTAAGGGAATATCAAATATTGGAAAAGAGAGACA
1 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACA
* *
229894 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAAAGAGACA
1 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACA
* * *
229942 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGAAGAAGTGAGACT
1 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACA
* * *
229990 TGTTCCTCTTACTTTGAAGGGAATAACAAATCTTGGAGAAGAGAGACA
1 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACA
* *
230038 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACT
1 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACA
* *
230086 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAATAGAGACT
1 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACA
* *
230134 TGTTCCGCTTACT-TGAAGGGAATATCAAATCTTTGAGAAGAGAGATA
1 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACA
* *
230181 TGTTCCACTTACTCTGAAGGGAATATCATATC-TGGAG
1 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAG
230218 GTATTGATTC
Statistics
Matches: 295, Mismatches: 28, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
47 46 0.16
48 249 0.84
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (48 bp):
TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACA
Found at i:230951 original size:149 final size:150
Alignment explanation
Indices: 230613--230954 Score: 458
Period size: 149 Copynumber: 2.3 Consensus size: 150
230603 ATGATTTAAG
* * * *
230613 CATCATGCTCGAAAGA-CTTACT-GATGGCCTGAAGGACTTATAAATTTTGGAAATAGTTTACTA
1 CATCATGC-CCAAAGATCTTA-TGGATGACCCGAAGGACTTATCAATTTTGGAAATAGTTTACTA
*
230676 AGTAAGAAACATTTCTTACTTTTCAAAAATTTTAATTTTCAAATTTAGATGAGAAACCTTTCTCA
64 AGTAAGAAACATTTCTTACTTTTCAAAAATTTTAATTTTCAAATTTAAATGAGAAACCTTTCTCA
* *
230741 TATTTTAATAGACATTTGAAAA
129 TATTTCAATAGACATGTGAAAA
*
230763 CATCCTGCCCAAAGATCTTATGGATGACCCGAAGGACTTATCAATTTTGGAAATAGTTTACTAAG
1 CATCATGCCCAAAGATCTTATGGATGACCCGAAGGACTTATCAATTTTGGAAATAGTTTACTAAG
* * * *
230828 TAAGAAACCTTTCTTACTTTTCAAAAA-TTTCATTTTTAGATTTAAATGAGAAACCTTTCTCATA
66 TAAGAAACATTTCTTACTTTTCAAAAATTTTAATTTTCAAATTTAAATGAGAAACCTTTCTCATA
* *
230892 TTTCGATGGACATGTGAAAA
131 TTTCAATAGACATGTGAAAA
** * * *
230912 CATCATGCCTGAAGGTCTTATGGAT-AGCTCGAATGACTTATCA
1 CATCATGCCCAAAGATCTTATGGATGA-CCCGAAGGACTTATCA
230955 TCTTGCTTGA
Statistics
Matches: 169, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
148 1 0.01
149 91 0.54
150 77 0.46
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (150 bp):
CATCATGCCCAAAGATCTTATGGATGACCCGAAGGACTTATCAATTTTGGAAATAGTTTACTAAG
TAAGAAACATTTCTTACTTTTCAAAAATTTTAATTTTCAAATTTAAATGAGAAACCTTTCTCATA
TTTCAATAGACATGTGAAAA
Found at i:238937 original size:11 final size:11
Alignment explanation
Indices: 238921--238947 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
238911 AAACGACCCT
238921 AAACACCTCTA
1 AAACACCTCTA
238932 AAACACCTCTA
1 AAACACCTCTA
238943 AAACA
1 AAACA
238948 ATCTCCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (11 bp):
AAACACCTCTA
Found at i:241900 original size:2 final size:2
Alignment explanation
Indices: 241893--241922 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
241883 GTATGAATGA
241893 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
241923 GAAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:243264 original size:60 final size:59
Alignment explanation
Indices: 243125--243264 Score: 140
Period size: 60 Copynumber: 2.3 Consensus size: 59
243115 ATAAATATTC
* * * *
243125 GAGTGACTATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAGTAACTTCCTATAGGT
1 GAGTGACCATTTTGT-ACTTATAATAGTTAAGAGACTCAACAAAGTAACTTCCTATAGAT
* * * *
243185 GAGAGACCACTTTTTTACTTATAATAGTTAAGAGACTCAATAAAGTAA-TATCGTATA-AT
1 GAGTGACCA-TTTTGTACTTATAATAGTTAAGAGACTCAACAAAGTAACT-TCCTATAGAT
*
243244 CGGGTGACCATTTGTGTACTT
1 -GAGTGACCATTT-TGTACTT
243265 TACCCTTAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
59 5 0.08
60 55 0.85
61 5 0.08
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (59 bp):
GAGTGACCATTTTGTACTTATAATAGTTAAGAGACTCAACAAAGTAACTTCCTATAGAT
Found at i:244729 original size:15 final size:16
Alignment explanation
Indices: 244689--244732 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
244679 TTTAGAAATC
*
244689 TTTAATCAAATATATT
1 TTTAATAAAATATATT
*
244705 TTTAATAAAATTTATT
1 TTTAATAAAATATATT
244721 TTTAA-AAAATAT
1 TTTAATAAAATAT
244733 TTAGAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAATAAAATATATT
Found at i:244879 original size:15 final size:16
Alignment explanation
Indices: 244839--244882 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
244829 TTTAGAAATC
*
244839 TTTAATCAAATATATT
1 TTTAATAAAATATATT
*
244855 TTTAATAAAATTTATT
1 TTTAATAAAATATATT
244871 TTTAA-AAAATAT
1 TTTAATAAAATAT
244883 TTAGAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAATAAAATATATT
Found at i:244894 original size:150 final size:151
Alignment explanation
Indices: 244619--244924 Score: 598
Period size: 150 Copynumber: 2.0 Consensus size: 151
244609 TATTTAGTCA
244619 ATTT-ATTAACTTTGACTCATTATTATTTAAAATTCATTATTCATAAAAATATATATATATTTTA
1 ATTTAATTAACTTTGACTCATTATTATTTAAAATTCATTATTCATAAAAATATATATATATTTTA
244683 GAAATCTTTAATCAAATATATTTTTAATAAAATTTATTTTTAAAAAATATTTAGAATAATTATGA
66 GAAATCTTTAATCAAATATATTTTTAATAAAATTTATTTTTAAAAAATATTTAGAATAATTATGA
244748 -CAAATTTTAAAAATTTTGAC
131 TCAAATTTTAAAAATTTTGAC
244768 ATTTAATTAACTTTGACTCATTATTATTTAAAATTCATTATTCATAAAAATATATATATATTTTA
1 ATTTAATTAACTTTGACTCATTATTATTTAAAATTCATTATTCATAAAAATATATATATATTTTA
244833 GAAATCTTTAATCAAATATATTTTTAATAAAATTTATTTTTAAAAAATATTTAGAATAATTATGA
66 GAAATCTTTAATCAAATATATTTTTAATAAAATTTATTTTTAAAAAATATTTAGAATAATTATGA
244898 TCAAATTTTAAAAATTTTGAC
131 TCAAATTTTAAAAATTTTGAC
244919 ATTTAA
1 ATTTAA
244925 AAAGTTAAAT
Statistics
Matches: 155, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
149 4 0.03
150 125 0.81
151 26 0.17
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (151 bp):
ATTTAATTAACTTTGACTCATTATTATTTAAAATTCATTATTCATAAAAATATATATATATTTTA
GAAATCTTTAATCAAATATATTTTTAATAAAATTTATTTTTAAAAAATATTTAGAATAATTATGA
TCAAATTTTAAAAATTTTGAC
Found at i:245503 original size:29 final size:30
Alignment explanation
Indices: 245477--245553 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
245467 TGATAAATAA
*
245477 TTTACGTAAAATGGATTA-TCT-AAAAATTG
1 TTTACGTAAAATGAATTACT-TGAAAAATTG
*
245506 TTTATGTAAAATGAATTACTTGAAAAATTG
1 TTTACGTAAAATGAATTACTTGAAAAATTG
245536 TTTAACGTAAAATGAATT
1 TTT-ACGTAAAATGAATT
245554 GCCTAAAACT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 17 0.40
30 12 0.29
31 13 0.31
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.39
Consensus pattern (30 bp):
TTTACGTAAAATGAATTACTTGAAAAATTG
Found at i:245572 original size:29 final size:29
Alignment explanation
Indices: 245477--245577 Score: 96
Period size: 29 Copynumber: 3.4 Consensus size: 29
245467 TGATAAATAA
* *
245477 TTTACGTAAAATGGATTATCTAAAAAT-T
1 TTTACGTAAAATGAATTACCTAAAAATGT
* *
245505 GTTTATGTAAAATGAATTACTTGAAAAATTGT
1 -TTTACGTAAAATGAATTACCT-AAAAA-TGT
* * *
245537 TTAACGTAAAATGAATTGCCTAAAACTGT
1 TTTACGTAAAATGAATTACCTAAAAATGT
*
245566 TTTACGTGAAAT
1 TTTACGTAAAAT
245578 AAATAATATT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 30 0.52
30 9 0.16
31 18 0.31
32 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (29 bp):
TTTACGTAAAATGAATTACCTAAAAATGT
Found at i:245709 original size:2 final size:2
Alignment explanation
Indices: 245702--245761 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
245692 ACCGAAATAA
*
245702 AT AT AT AT AT TT AT AT AT AT -T AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
245742 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
245762 GTACAATTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:245727 original size:19 final size:19
Alignment explanation
Indices: 245703--245759 Score: 105
Period size: 19 Copynumber: 3.0 Consensus size: 19
245693 CCGAAATAAA
*
245703 TATATATATTTATATATAT
1 TATATATATATATATATAT
245722 TATATATATATATATATAT
1 TATATATATATATATATAT
245741 TATATATATATATATATAT
1 TATATATATATATATATAT
245760 ATGTACAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATATATATATATATAT
Found at i:247769 original size:19 final size:18
Alignment explanation
Indices: 247745--247788 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
247735 AAGTATATAT
247745 TAATATAATATTAAAAATA
1 TAATAT-ATATTAAAAATA
*
247764 TAATAT-TATTAAAATTA
1 TAATATATATTAAAAATA
*
247781 TATTATAT
1 TAATATAT
247789 GTATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATATATATTAAAAATA
Found at i:253023 original size:2 final size:2
Alignment explanation
Indices: 253016--253044 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
253006 CAAGAGGAGG
253016 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
253045 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:253051 original size:4 final size:4
Alignment explanation
Indices: 253044--253100 Score: 60
Period size: 4 Copynumber: 14.2 Consensus size: 4
253034 TCTCTCTCTC
* * * * *
253044 TATA TATA TATA TATA TATA TATC TATA TCTA TATA TCTA TCTA TCTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
253092 TCTA TATA T
1 TATA TATA T
253101 GTCTGTCTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:257127 original size:2 final size:2
Alignment explanation
Indices: 257122--257157 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
257112 TATTTCTGTG
257122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
257158 AAGTCTAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:260495 original size:20 final size:20
Alignment explanation
Indices: 260470--260507 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
260460 TTTGGTTCAC
260470 AGAATGTAAGATTACCAGTA
1 AGAATGTAAGATTACCAGTA
260490 AGAATGTAAGATTACCAG
1 AGAATGTAAGATTACCAG
260508 GGAATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.24
Consensus pattern (20 bp):
AGAATGTAAGATTACCAGTA
Found at i:260718 original size:2 final size:2
Alignment explanation
Indices: 260711--260757 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
260701 TTTAAATTAA
*
260711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
260753 AT AT A
1 AT AT A
260758 AAAGGGTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:264394 original size:20 final size:20
Alignment explanation
Indices: 264357--264394 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
264347 GGTCGTTTTT
*
264357 AGCCGTTAGGGATGATTTGG
1 AGCCGTTAGGGATAATTTGG
264377 AGCCGTT-GGGTATAATTT
1 AGCCGTTAGGG-ATAATTT
264395 TTATGCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.21, C:0.11, G:0.34, T:0.34
Consensus pattern (20 bp):
AGCCGTTAGGGATAATTTGG
Found at i:265371 original size:18 final size:18
Alignment explanation
Indices: 265344--265386 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
265334 TTAAAAAATT
*
265344 GATATTAATTGTTAGAGA
1 GATATCAATTGTTAGAGA
265362 GATATCAATTGTTAGAGA
1 GATATCAATTGTTAGAGA
265380 GATATCA
1 GATATCA
265387 TTTGCGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (18 bp):
GATATCAATTGTTAGAGA
Found at i:266010 original size:21 final size:21
Alignment explanation
Indices: 265978--266024 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
265968 TTCAAGCTTA
265978 ATTTTCAAATCA-TGATTTTC
1 ATTTTCAAATCATTGATTTTC
*
265998 ATTTTCTAAATCATTGATTTTG
1 ATTTTC-AAATCATTGATTTTC
266020 ATTTT
1 ATTTT
266025 TGAAAGCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.25
21 6 0.25
22 12 0.50
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTTTCAAATCATTGATTTTC
Found at i:274216 original size:21 final size:22
Alignment explanation
Indices: 274187--274232 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
274177 CAAGCTTAAC
274187 TTTCAAATCA-AGATTTT-ATT
1 TTTCAAATCATAGATTTTGATT
*
274207 TTTCTAAATCATTGATTTTGATT
1 TTTC-AAATCATAGATTTTGATT
274230 TTT
1 TTT
274233 GAAAGATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 6 0.27
22 6 0.27
23 6 0.27
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.57
Consensus pattern (22 bp):
TTTCAAATCATAGATTTTGATT
Found at i:278850 original size:20 final size:20
Alignment explanation
Indices: 278827--278874 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
278817 TTTCATATAG
278827 TATCAATATTGTAAGAATAA
1 TATCAATATTGTAAGAATAA
*
278847 TATCAATATTGTAAGAATAG
1 TATCAATATTGTAAGAATAA
278867 TATCAATA
1 TATCAATA
278875 CTACTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (20 bp):
TATCAATATTGTAAGAATAA
Found at i:282357 original size:46 final size:46
Alignment explanation
Indices: 282283--282501 Score: 253
Period size: 46 Copynumber: 4.8 Consensus size: 46
282273 TAATATACCA
* ** * * *
282283 TTATGTATTTTCATTGGTGGAATCCTTTCATTCCAATTATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCACCG
* * *
282329 TTAAT-CATTTTCATTTATGGCATTCTTTCATGCCTATAATGTACCG
1 TT-ATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCACCG
* *
282375 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATACACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCACCG
* * **
282421 -TATGCATTTTCATTTATGGAATCCTTTCATGCCGATAATGCATTG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCACCG
* * *
282466 TTATACATTTTCATTTATGACATTCTTTCATGCCAA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAA
282502 AGACATTTAA
Statistics
Matches: 148, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
45 43 0.29
46 103 0.70
47 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.43
Consensus pattern (46 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCACCG
Found at i:282459 original size:91 final size:92
Alignment explanation
Indices: 282273--282501 Score: 264
Period size: 91 Copynumber: 2.5 Consensus size: 92
282263 TATATGTCGT
* * * ** * * * *
282273 TAATATACCATTATGTATTTTCATTGGTGGAATCCTTTCATTCCAATTATGCACCGTTAATCATT
1 TAATGTACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATACACCGTTAATCATT
* * *
282338 TTCATTTATGGCATTCTTTCATGCCTA
66 TTCATTTATGGAATCCTTTCATGCCGA
*
282365 TAATGTACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATACACCG-T-ATGCAT
1 TAATGTACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATACACCGTTAAT-CAT
282428 TTTCATTTATGGAATCCTTTCATGCCGA
65 TTTCATTTATGGAATCCTTTCATGCCGA
* ** * * *
282456 TAATGCATTGTTATACATTTTCATTTATGACATTCTTTCATGCCAA
1 TAATGTACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCAA
282502 AGACATTTAA
Statistics
Matches: 116, Mismatches: 20, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
90 2 0.02
91 68 0.59
92 46 0.40
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (92 bp):
TAATGTACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATACACCGTTAATCATT
TTCATTTATGGAATCCTTTCATGCCGA
Found at i:282600 original size:81 final size:81
Alignment explanation
Indices: 282506--283304 Score: 1037
Period size: 81 Copynumber: 9.9 Consensus size: 81
282496 TGCCAAAGAC
* * * * *
282506 ATTTAATCTTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
282571 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
*
282587 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGGCAATT-A
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
*
282651 TCTTTAACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * *
282667 ATTTAACCTTTCATCTAACTGGCATGATTGACATCTTTCTGTCAAATGCACAACTAGGCATTTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
282732 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * * * * * * *
282748 ATTTATCCTTTCATCTAATTGGCATGATTGACACCTTTCTTTTAAATACATAACTAGACAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
*
282813 TCTTTTACTCAAATGT
66 TCTTTTACTCAAAGGT
* * * * * *
282829 ATTTAGCCTTTCCTCTAACTGCCATGATTGGCACCTTTCTATCAAATGCACATCTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
* * *
282894 TCTTTTACTGAAGGGC
66 TCTTTTACTCAAAGGT
* * *
282910 ATTTAACATTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGACAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
*
282975 TTTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * * * * * *
282991 ATTTAACCTTTCATGTAACTGGCATGATTAACACCTATATATAAAATGCATAGCTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
*
283056 TCTTTTACTCAAATGT
66 TCTTTTACTCAAAGGT
* * * * * * *
283072 ATTTAATCTTTCATCTAATTGTCATGATTGATACCTTTATTTCAAATGCACAGCTAGACAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
*
283137 TCTTTTACTCAAAAGT
66 TCTTTTACTCAAAGGT
* * * **
283153 GTTTAACCTTTCATCTAACT-GCATGATTGACACATTTCTGTCAAATCCACATATAGGCAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
* *
283217 TCTTTTACTGAAAAGT
66 TCTTTTACTCAAAGGT
* * * *
283233 ATGTAACCTTTCATCTAACTGGTATGATTGACACATTTCTGTCAAATGCATAGCTAGGCAATTAG
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTA-
283298 A-CTTTTA
65 ATCTTTTA
283305 ATTTAAAACA
Statistics
Matches: 623, Mismatches: 92, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
80 145 0.23
81 477 0.77
82 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (81 bp):
ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
TCTTTTACTCAAAGGT
Found at i:283847 original size:21 final size:21
Alignment explanation
Indices: 283817--283878 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
283807 CCTTCCTTTT
*
283817 AGTATCGATACTAATTGCGTC
1 AGTATCGATACTAATTGCATC
* *
283838 AGTGTCGATACTAATTGTATC
1 AGTATCGATACTAATTGCATC
283859 AGTATCGATACT-ATT-CATC
1 AGTATCGATACTAATTGCATC
283878 A
1 A
283879 TAATTCTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 4 0.11
20 3 0.08
21 29 0.81
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (21 bp):
AGTATCGATACTAATTGCATC
Found at i:288512 original size:23 final size:23
Alignment explanation
Indices: 288463--288515 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
288453 AAAATTATTC
* * **
288463 AAAAACCATGAAATCCTGATATT
1 AAAAACCATGAAAACCTAATAAG
288486 AAAAACCATGAAAACCTAATAAG
1 AAAAACCATGAAAACCTAATAAG
288509 AAAAACC
1 AAAAACC
288516 CGATCACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.57, C:0.19, G:0.08, T:0.17
Consensus pattern (23 bp):
AAAAACCATGAAAACCTAATAAG
Found at i:291795 original size:21 final size:22
Alignment explanation
Indices: 291769--291868 Score: 107
Period size: 22 Copynumber: 4.5 Consensus size: 22
291759 ATATATATAT
291769 ATATATATTATAG-TTTTGAAA
1 ATATATATTATAGTTTTTGAAA
* *
291790 ATATATAATATAGTTTTTAAAA
1 ATATATATTATAGTTTTTGAAA
* *
291812 AAACATATTATA-TAGTTTTG-AA
1 ATATATATTATAGT--TTTTGAAA
291834 ATATATATATATAGTTTTTGAAA
1 ATATATAT-TATAGTTTTTGAAA
*
291857 ATATATAATATA
1 ATATATATTATA
291869 AATATTAGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
21 13 0.20
22 33 0.52
23 17 0.27
24 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (22 bp):
ATATATATTATAGTTTTTGAAA
Found at i:291853 original size:67 final size:67
Alignment explanation
Indices: 291767--291990 Score: 195
Period size: 72 Copynumber: 3.2 Consensus size: 67
291757 ATATATATAT
291767 ATATATATATTATAG-TTTTGAAAATATATAATATAGTTTTTAAAAAAACATATTATATAGTTTT
1 ATATATATA-TATAGTTTTTGAAAATATATAATATAGTTTTTAAAAAAACATATTATATAGTTTT
291831 GAA
65 GAA
* * *
291834 ATATATATATATAGTTTTTGAAAATATATAATATAAATATTAGTTTTAAAAAACATA-TA-AT-T
1 ATATATATATATAGTTTTTGAAAATATATAATAT--A-GTT--TTTAAAAAAACATATTATATAG
291896 TTTTGAAAA
61 TTTTG--AA
* * * * * *
291905 CATATATAATATATAATTTTTTAAAATGTATTATATGGTTTTTGAAAATATAATATATTATATAG
1 -ATATAT-ATATATAGTTTTTGAAAATATATAATATAGTTTTT-AAAA-A-AACATATTATATAG
*
291970 TTTTTAAA
61 -TTTTGAA
291978 ATATATAGTATAT
1 ATATATA-TATAT
291991 TATTACTATG
Statistics
Matches: 126, Mismatches: 13, Indels: 31
0.74 0.08 0.18
Matches are distributed among these distances:
66 5 0.04
67 28 0.22
68 3 0.02
69 9 0.07
70 7 0.06
71 10 0.08
72 32 0.25
73 28 0.22
75 4 0.03
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (67 bp):
ATATATATATATAGTTTTTGAAAATATATAATATAGTTTTTAAAAAAACATATTATATAGTTTTG
AA
Found at i:291891 original size:29 final size:30
Alignment explanation
Indices: 291833--291894 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
291823 ATAGTTTTGA
* ** *
291833 AATATATATATATAGTTTTTGAAAATATAT
1 AATATAAATATATAGTTTTAAAAAACATAT
291863 AATATAAATAT-TAGTTTTAAAAAACATAT
1 AATATAAATATATAGTTTTAAAAAACATAT
291892 AAT
1 AAT
291895 TTTTTGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
AATATAAATATATAGTTTTAAAAAACATAT
Found at i:291963 original size:27 final size:28
Alignment explanation
Indices: 291933--291993 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
291923 TTTTAAAATG
*
291933 TATTATATGGTTTTTGAAAATATA-A-TA
1 TATTATATAGTTTTT-AAAATATATAGTA
291960 TATTATATAGTTTTTAAAATATATAGTA
1 TATTATATAGTTTTTAAAATATATAGTA
291988 TATTAT
1 TATTAT
291994 TACTATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 8 0.26
27 15 0.48
28 8 0.26
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (28 bp):
TATTATATAGTTTTTAAAATATATAGTA
Found at i:293271 original size:45 final size:45
Alignment explanation
Indices: 293205--293475 Score: 355
Period size: 45 Copynumber: 6.0 Consensus size: 45
293195 ATGCACTTTA
* * *
293205 AACTATATCAAACTTTTCTGTTGATAATGCACCCATATGCATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* * * *
293250 AAATATAGTATACTTTTCTGTTAATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
** * *
293295 AACTACCGCATACTTTTCTGTTTATAATGTA-CCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* * *
293339 AACTATAGCATATTTTTCTGTTGATAATGCACCCATATGCATTTA
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* *
293384 AACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* * * *
293429 AACTACAACATACTTTTTTGTTGATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
293474 AA
1 AA
293476 TTTGGCATCC
Statistics
Matches: 197, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
44 39 0.20
45 158 0.80
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (45 bp):
AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
Found at i:293397 original size:134 final size:135
Alignment explanation
Indices: 293218--293475 Score: 430
Period size: 134 Copynumber: 1.9 Consensus size: 135
293208 TATATCAAAC
*
293218 TTTTCTGTTGATAATGCACCCATATGCATTTCAAATATAGTATACTTTTCTGTTAATAATGTACC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAAATATAGTATACTTTTCTGTTAATAATGCACC
** *
293283 CATATACATTTCAACTACCGCATACTTTTCTGTTTATAATGTA-CCATATACATTTCAACTATAG
66 CATATACATTTCAACTACAACATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAG
293347 CATAT
131 CATAT
*
293352 TTTTCTGTTGATAATGCACCCATATGCATTT-AAACTATAGTATACTTTTCTGTTGATAATGCAC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAAA-TATAGTATACTTTTCTGTTAATAATGCAC
* *
293416 CCATATGCATTTCAACTACAACATACTTTTTTGTTGATAATGTACCCATATACATTTCAA
65 CCATATACATTTCAACTACAACATACTTTTCTGTTGATAATGTACCCATATACATTTCAA
293476 TTTGGCATCC
Statistics
Matches: 115, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
133 3 0.03
134 97 0.84
135 15 0.13
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (135 bp):
TTTTCTGTTGATAATGCACCCATATGCATTTCAAATATAGTATACTTTTCTGTTAATAATGCACC
CATATACATTTCAACTACAACATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAG
CATAT
Found at i:293499 original size:134 final size:134
Alignment explanation
Indices: 293227--293514 Score: 395
Period size: 134 Copynumber: 2.2 Consensus size: 134
293217 CTTTTCTGTT
*
293227 GATAATGCACCCATATGCATTTCAAATATAGTATACTTTTCTGTTAATAATGTACCCATATACAT
1 GATAATGCACCCATATGCATTTCAAATATAGTATACTTTTCTGTTAATAATGCACCCATATACAT
** * **
293292 TTCAACTACCGCATACTTTTCTGTTTATAATGTACCATATACATTTCAACTATAGCATATTTTTC
66 TTCAACTACAACATACTTTTCTGTTGATAATGTACCATATACATTTCAACTATAGCATACCTTTC
**
293357 TGTT
131 TGCC
* *
293361 GATAATGCACCCATATGCATTT-AAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
1 GATAATGCACCCATATGCATTTCAAA-TATAGTATACTTTTCTGTTAATAATGCACCCATATACA
* * *
293425 TTTCAACTACAACATACTTTTTTGTTGATAATGTACCCATATACATTTCAA-TTTGGCAT-CCTT
65 TTTCAACTACAACATACTTTTCTGTTGATAATGTA-CCATATACATTTCAACTATAGCATACCTT
293488 TCATGCC
129 TC-TGCC
*
293495 GATAATACA-CCATATGCATT
1 GATAATGCACCCATATGCATT
293515 AGTATTTTCA
Statistics
Matches: 137, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
133 18 0.13
134 104 0.76
135 15 0.11
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.39
Consensus pattern (134 bp):
GATAATGCACCCATATGCATTTCAAATATAGTATACTTTTCTGTTAATAATGCACCCATATACAT
TTCAACTACAACATACTTTTCTGTTGATAATGTACCATATACATTTCAACTATAGCATACCTTTC
TGCC
Found at i:299273 original size:45 final size:45
Alignment explanation
Indices: 299220--299527 Score: 381
Period size: 45 Copynumber: 6.8 Consensus size: 45
299210 ACTATATCAT
* * *
299220 ACTTTTCTGTTGATAATGCACTCATATGCATTTCAACTATAATAC
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAATAC
**
299265 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTACCGCATAC
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTA--TAATAC
* * *
299312 -C-TTTCTGTTGATAATGTACCTATATACATTTCAACTA-AAGCAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAA-TAC
* * * *
299355 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACCATAGTAC
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAATAC
* * * * *
299400 ACTTTTCTGTTGATAATGCACCCATATGCATTTTAACTA-CATCAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAAT-AC
* *
299445 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAATAC
299490 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACT
299528 TTGGCATCCT
Statistics
Matches: 229, Mismatches: 26, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 2 0.01
45 218 0.95
46 3 0.01
47 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (45 bp):
ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAATAC
Found at i:299326 original size:90 final size:89
Alignment explanation
Indices: 299209--299527 Score: 431
Period size: 90 Copynumber: 3.6 Consensus size: 89
299199 ATGAACTTTA
* * * *
299209 AACTATATCATACTTTTCTGTTGATAATGCACTCATATGCATTTCAACTATAATACACTTTTCTG
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTA-AATATACTTTTCTG
299274 TTGATAATGTACCCATATACATTTC
65 TTGATAATGTACCCATATACATTTC
** * * * *
299299 AACTACCGCATACCTTTCTGTTGATAATGTACCTATATACATTTCAACTAAAGCATACTTTTCTG
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTAAA-TATACTTTTCTG
* *
299364 TTGATAATGCACCCATATGCATTTC
65 TTGATAATGTACCCATATACATTTC
* * * * * *
299389 AACCATAGTACACTTTTCTGTTGATAATGCACCCATATGCATTTTAACTACATCATACTTTTCTG
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTAAAT-ATACTTTTCTG
299454 TTGATAATGTACCCATATACATTTC
65 TTGATAATGTACCCATATACATTTC
* *
299479 AACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAACT
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAACT
299528 TTGGCATCCT
Statistics
Matches: 196, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
89 2 0.01
90 194 0.99
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (89 bp):
AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTAAATATACTTTTCTGT
TGATAATGTACCCATATACATTTC
Found at i:299402 original size:135 final size:135
Alignment explanation
Indices: 299217--299526 Score: 494
Period size: 135 Copynumber: 2.3 Consensus size: 135
299207 TAAACTATAT
* *
299217 CATACTTTTCTGTTGATAATGCACTCATATGCATTTCAACTATAATACACTTTTCTGTTGATAAT
1 CATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACCATAATACACTTTTCTGTTGATAAT
* * *
299282 GTACCCATATACATTTCAACTACCGCATACCTTTCTGTTGATAATGTACCTATATACATTTCAAC
66 GCACCCATATACATTTCAACTACAGCATACCTTTCTGTTGATAATGTACCCATATACATTTCAAC
299347 TAAAG
131 TAAAG
*
299352 CATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACCATAGTACACTTTTCTGTTGATAAT
1 CATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACCATAATACACTTTTCTGTTGATAAT
* * * *
299417 GCACCCATATGCATTTTAACTACATCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
66 GCACCCATATACATTTCAACTACAGCATACCTTTCTGTTGATAATGTACCCATATACATTTCAAC
*
299482 TATAG
131 TAAAG
* * *
299487 TATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
1 CATACTTTTCTGTTGATAATGCACCCATATGCATTTCAAC
299527 TTTGGCATCC
Statistics
Matches: 161, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
135 161 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (135 bp):
CATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACCATAATACACTTTTCTGTTGATAAT
GCACCCATATACATTTCAACTACAGCATACCTTTCTGTTGATAATGTACCCATATACATTTCAAC
TAAAG
Found at i:299550 original size:45 final size:45
Alignment explanation
Indices: 299231--299566 Score: 228
Period size: 45 Copynumber: 7.5 Consensus size: 45
299221 CTTTTCTGTT
* * * * **
299231 GATAATGCACTCATATGCATTTCAACTATA--ATACACTTTTCTGTT
1 GATAATGTACCCATATACATTTCAACTATAGCATAC-C-TTCCTGCC
** * **
299276 GATAATGTACCCATATACATTTCAACTACCGCATACCTTTCTGTT
1 GATAATGTACCCATATACATTTCAACTATAGCATACCTTCCTGCC
* * * * **
299321 GATAATGTACCTATATACATTTCAACTAAAGCATACTTTTCTGTT
1 GATAATGTACCCATATACATTTCAACTATAGCATACCTTCCTGCC
* * * * * * * **
299366 GATAATGCACCCATATGCATTTCAACCATAGTACACTTTTCTGTT
1 GATAATGTACCCATATACATTTCAACTATAGCATACCTTCCTGCC
* * * * * * * **
299411 GATAATGCACCCATATGCATTTTAACTACATCATACTTTTCTGTT
1 GATAATGTACCCATATACATTTCAACTATAGCATACCTTCCTGCC
* * * **
299456 GATAATGTACCCATATACATTTCAACTATAGTATACTTTTCTGTT
1 GATAATGTACCCATATACATTTCAACTATAGCATACCTTCCTGCC
* *
299501 GATAATGTACCCATATACATTTCAACTTTGGCAT-CCTTCCATGCC
1 GATAATGTACCCATATACATTTCAACTATAGCATACCTTCC-TGCC
* *
299546 GATAATGCACCCATATGCATT
1 GATAATGTACCCATATACATT
299567 AGTATTTTCA
Statistics
Matches: 251, Mismatches: 37, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
44 4 0.02
45 242 0.96
46 1 0.00
47 4 0.02
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (45 bp):
GATAATGTACCCATATACATTTCAACTATAGCATACCTTCCTGCC
Found at i:299550 original size:135 final size:135
Alignment explanation
Indices: 299217--299566 Score: 434
Period size: 135 Copynumber: 2.6 Consensus size: 135
299207 TAAACTATAT
* * * * * * **
299217 CATACTTTTCTGTTGATAATGCACTCATATGCATTTCAACTATAATACACTTTTCTGTTGATAAT
1 CATACTTTTCTGTTGATAATGCACCCATATACATTTCAACCATAGTACACCTTCCTGCCGATAAT
* * * *
299282 GTACCCATATACATTTCAACTACCGCATACCTTTCTGTTGATAATGTACCTATATACATTTCAAC
66 GCACCCATATGCATTTCAACTACAGCATACCTTTCTGTTGATAATGTACCCATATACATTTCAAC
299347 TAAAG
131 TAAAG
* * * **
299352 CATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACCATAGTACACTTTTCTGTTGATAAT
1 CATACTTTTCTGTTGATAATGCACCCATATACATTTCAACCATAGTACACCTTCCTGCCGATAAT
* * *
299417 GCACCCATATGCATTTTAACTACATCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
66 GCACCCATATGCATTTCAACTACAGCATACCTTTCTGTTGATAATGTACCCATATACATTTCAAC
*
299482 TATAG
131 TAAAG
* * * * *
299487 TATACTTTTCTGTTGATAATGTACCCATATACATTTCAA-CTTTG-GCATCCTTCCATGCCGATA
1 CATACTTTTCTGTTGATAATGCACCCATATACATTTCAACCATAGTACA-CCTTCC-TGCCGATA
299550 ATGCACCCATATGCATT
64 ATGCACCCATATGCATT
299567 AGTATTTTCA
Statistics
Matches: 192, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
133 2 0.01
134 7 0.04
135 183 0.95
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (135 bp):
CATACTTTTCTGTTGATAATGCACCCATATACATTTCAACCATAGTACACCTTCCTGCCGATAAT
GCACCCATATGCATTTCAACTACAGCATACCTTTCTGTTGATAATGTACCCATATACATTTCAAC
TAAAG
Found at i:300005 original size:20 final size:20
Alignment explanation
Indices: 299977--300029 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
299967 TTGATTCTGA
* *
299977 AGTATCGATA-TTACTACCCT
1 AGTACCGATACTT-CTACACT
299997 AGTACCGATACTTCTACACT
1 AGTACCGATACTTCTACACT
300017 AGGGTACCGATAC
1 A--GTACCGATAC
300030 CCCTACTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 16 0.57
21 2 0.07
22 10 0.36
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (20 bp):
AGTACCGATACTTCTACACT
Found at i:300123 original size:22 final size:22
Alignment explanation
Indices: 300080--300123 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
300070 ATGGTATCGA
* *
300080 TACCTTACCATGGTATCAATAC
1 TACCTTACCAAGGTACCAATAC
* *
300102 TACCTTACTAAGGTACCGATAC
1 TACCTTACCAAGGTACCAATAC
300124 CCCCTTAAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (22 bp):
TACCTTACCAAGGTACCAATAC
Found at i:303565 original size:32 final size:32
Alignment explanation
Indices: 303501--303570 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
303491 GATGGGGGTA
* * *
303501 TAATTTAGTTATATCAATATCGATTTTTATTT
1 TAATTTAGTTATATCAATATCAATATTGATTT
303533 TAATTTAGTTATATCAA-ATTCAATATTGATTT
1 TAATTTAGTTATATCAATA-TCAATATTGATTT
*
303565 TTATTT
1 TAATTT
303571 TTATAGACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 1 0.03
32 32 0.97
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (32 bp):
TAATTTAGTTATATCAATATCAATATTGATTT
Found at i:313742 original size:13 final size:13
Alignment explanation
Indices: 313706--313744 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
313696 CAATGACGCC
313706 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
313719 AATGTGTGTCATA
1 AATGCGCGTCATA
313732 AATGCGCGTCATA
1 AATGCGCGTCATA
313745 GATTTATGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:313753 original size:97 final size:97
Alignment explanation
Indices: 313620--313801 Score: 256
Period size: 97 Copynumber: 1.9 Consensus size: 97
313610 ATTTAAGTCG
* * * * *
313620 TAAATGTAAGTCATAAATGCGTGTCATAAATTTATGACACTCAAATGTGTGTCGTCTTCATTTAT
1 TAAATGTAAGTCATAAATGCGCGTCATAAATTTATGACACACAAATGCGTGTCATCTGCATTTAT
*
313685 GATGGTAGCTTCAATGACGCCAATGCGCGTCA
66 GACGGTAGCTTCAATGACGCCAATGCGCGTCA
** * * *
313717 TAAATGTGTGTCATAAATGCGCGTCATAGATTTATGACACACAATTGCGTGTCATCTGGATTTAT
1 TAAATGTAAGTCATAAATGCGCGTCATAAATTTATGACACACAAATGCGTGTCATCTGCATTTAT
*
313782 GACGGTGGCTTCAATGACGC
66 GACGGTAGCTTCAATGACGC
313802 GCATTTGTGT
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
97 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (97 bp):
TAAATGTAAGTCATAAATGCGCGTCATAAATTTATGACACACAAATGCGTGTCATCTGCATTTAT
GACGGTAGCTTCAATGACGCCAATGCGCGTCA
Found at i:316671 original size:3 final size:3
Alignment explanation
Indices: 316637--316711 Score: 100
Period size: 3 Copynumber: 25.0 Consensus size: 3
316627 AGGCCTGTAA
* *
316637 AAT AAT TAT AAT ATAT AA- ATT AAT AA- AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
316681 AAT AAT AAT AAT AAT AAT AAT AAT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
316712 TATTTTTGTA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 3 0.05
3 55 0.86
4 6 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:324051 original size:21 final size:21
Alignment explanation
Indices: 324016--324063 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
324006 ATTATGTCTA
324016 TTAA-TTGCCTTTAATTTA-T
1 TTAATTTGCCTTTAATTTAGT
*
324035 TTGATTTGCCTTTTAATTTAGT
1 TTAATTTGCC-TTTAATTTAGT
324057 TTAATTT
1 TTAATTT
324064 TAATCCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 5 0.21
21 9 0.38
22 7 0.29
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.60
Consensus pattern (21 bp):
TTAATTTGCCTTTAATTTAGT
Found at i:328006 original size:18 final size:17
Alignment explanation
Indices: 327983--328093 Score: 120
Period size: 18 Copynumber: 6.5 Consensus size: 17
327973 AAAACACACA
*
327983 AAAAAGAAAGCAAAAAAG
1 AAAAA-AAAGAAAAAAAG
*
328001 AAAAAGAAGAAAAAAATG
1 AAAAAAAAGAAAAAAA-G
328019 AAAAAAAA-AAAAAAA-
1 AAAAAAAAGAAAAAAAG
*
328034 AAAAAAAA-AAAAAACG
1 AAAAAAAAGAAAAAAAG
*
328050 AAAAAAAAAAAAAAAAG
1 AAAAAAAAGAAAAAAAG
*
328067 AAAAAAAAAGAAGAAAAG
1 -AAAAAAAAGAAAAAAAG
328085 AAAGAAAAA
1 AAA-AAAAA
328094 TCAACTAAAC
Statistics
Matches: 81, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
15 14 0.17
16 8 0.10
17 26 0.32
18 33 0.41
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.01
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAAG
Found at i:328014 original size:17 final size:16
Alignment explanation
Indices: 327984--328093 Score: 104
Period size: 17 Copynumber: 6.8 Consensus size: 16
327974 AAACACACAA
*
327984 AAAAGAAAGCAAAAAAG
1 AAAA-AAAGAAAAAAAG
328001 AAAAAGAAGAAAAAAATG
1 AAAAA-AAGAAAAAAA-G
328019 AAAAAAA-AAAAAAA-
1 AAAAAAAGAAAAAAAG
*
328033 AAAAAAAAAAAAAAACG
1 AAAAAAAGAAAAAAA-G
328050 AAAAAAA-AAAAAAA-
1 AAAAAAAGAAAAAAAG
*
328064 AAGAAAAA-AAAAGAAG
1 AA-AAAAAGAAAAAAAG
328080 AAAAGAAAGAAAAA
1 AAAA-AAAGAAAAA
328094 TCAACTAAAC
Statistics
Matches: 81, Mismatches: 3, Indels: 18
0.79 0.03 0.18
Matches are distributed among these distances:
14 9 0.11
15 20 0.25
16 20 0.25
17 26 0.32
18 6 0.07
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.01
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAG
Found at i:328016 original size:12 final size:11
Alignment explanation
Indices: 327995--328093 Score: 96
Period size: 10 Copynumber: 8.7 Consensus size: 11
327985 AAAGAAAGCA
327995 AAAAAGAAAAAG
1 AAAAA-AAAAAG
*
328007 AAGAAAAAAATG
1 AA-AAAAAAAAG
328019 AAAAAAAAAA-
1 AAAAAAAAAAG
328029 AAAAAAAAAA-
1 AAAAAAAAAAG
*
328039 AAAAAAAAACG
1 AAAAAAAAAAG
328050 AAAAAAAAAA-
1 AAAAAAAAAAG
*
328060 AAAAAAGAAAAA
1 AAAAAA-AAAAG
328072 AAAAGAAGAAAAG
1 AAAA-AA-AAAAG
328085 AAAGAAAAA
1 AAA-AAAAA
328094 TCAACTAAAC
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
10 25 0.33
11 20 0.26
12 15 0.20
13 15 0.20
14 1 0.01
ACGTcount: A:0.88, C:0.01, G:0.10, T:0.01
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:328016 original size:30 final size:29
Alignment explanation
Indices: 327968--328093 Score: 116
Period size: 30 Copynumber: 4.2 Consensus size: 29
327958 GGAGAGATAT
* *
327968 AGAAAAAAACACACAAAAAAGAAAGCAAAAA
1 AGAAAAAAAGA-A-AAAAAAGAAAGAAAAAA
*
327999 AGAAAAAGAAGAAAAAAATGAAA-AAAAAA
1 AGAAAAA-AAGAAAAAAAAGAAAGAAAAAA
*
328028 A-AAAAAAA-AAAAAAAAAAAACGAAAAAAA
1 AGAAAAAAAGAAAAAAAAGAAA-G-AAAAAA
*
328057 AAAAAAAAAGAAAAAAAA-AGAAGAAAAGAA
1 AGAAAAAAAGAAAAAAAAGA-AAGAAAA-AA
328087 AGAAAAA
1 AGAAAAA
328094 TCAACTAAAC
Statistics
Matches: 81, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
26 10 0.12
27 2 0.02
28 5 0.06
29 17 0.21
30 26 0.32
31 18 0.22
32 3 0.04
ACGTcount: A:0.85, C:0.04, G:0.10, T:0.01
Consensus pattern (29 bp):
AGAAAAAAAGAAAAAAAAGAAAGAAAAAA
Found at i:328029 original size:31 final size:28
Alignment explanation
Indices: 327982--328093 Score: 118
Period size: 28 Copynumber: 3.9 Consensus size: 28
327972 AAAAACACAC
**
327982 AAAAAAGAAAGCAAAAAAGAAAAAGAAGA
1 AAAAAAGAAAAAAAAAAAGAAAAAGAA-A
* *
328011 AAAAAATGAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAA-G--AAAAAAAAAAAGAAAAAGAAA
328042 AAAAAACGAAAAAAAAAAA-AAAAAGAAA
1 AAAAAA-GAAAAAAAAAAAGAAAAAGAAA
* *
328070 AAAAAAGAAGAAAAGAAAGAAAAA
1 AAAAAAGAAAAAAAAAAAGAAAAA
328094 TCAACTAAAC
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
27 10 0.14
28 19 0.27
29 17 0.24
30 1 0.01
31 8 0.11
32 16 0.23
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.01
Consensus pattern (28 bp):
AAAAAAGAAAAAAAAAAAGAAAAAGAAA
Found at i:328093 original size:1 final size:1
Alignment explanation
Indices: 327994--328075 Score: 92
Period size: 1 Copynumber: 82.0 Consensus size: 1
327984 AAAAGAAAGC
* * * ** **
327994 AAAAAAGAAAAAGAAGAAAAAAATGAAAAAAAAAAAAAAAAAAAAAAAAAAAAACGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
328059 AAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAA
328076 GAAGAAAAGA
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.90, C:0.01, G:0.07, T:0.01
Consensus pattern (1 bp):
A
Found at i:329643 original size:12 final size:12
Alignment explanation
Indices: 329625--329660 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
329615 TATATACGTT
329625 CATGTGATATGA
1 CATGTGATATGA
*
329637 TATGTGATATGA
1 CATGTGATATGA
*
329649 CCTGTGATATGA
1 CATGTGATATGA
329661 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:336142 original size:64 final size:64
Alignment explanation
Indices: 336009--336130 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
335999 AATAAAGACG
* * ** *
336009 TCGAATGCAATTCGTGCATCAATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACA
1 TCGAATGCAATTCGTGCATCAATGCATAAGGAGTGCATCGATACATCCCAGCAATAATGAAACA
* *
336073 TCGAATGCAA-TCGGTGCATCGATGCATAAGGAGTGTATCGATACATCCCAGCAATAAT
1 TCGAATGCAATTC-GTGCATCAATGCATAAGGAGTGCATCGATACATCCCAGCAATAAT
336131 ACTACATCGA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 2 0.04
64 48 0.96
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (64 bp):
TCGAATGCAATTCGTGCATCAATGCATAAGGAGTGCATCGATACATCCCAGCAATAATGAAACA
Found at i:336494 original size:19 final size:20
Alignment explanation
Indices: 336457--336501 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
336447 ACATGCATAA
*
336457 GATAT-ATATATGTTCATGT
1 GATATGATATATGATCATGT
336476 GATATGATATATGAT-ATGT
1 GATATGATATATGATCATGT
336495 GATATGA
1 GATATGA
336502 CCTGTGATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.42
Consensus pattern (20 bp):
GATATGATATATGATCATGT
Found at i:336676 original size:15 final size:15
Alignment explanation
Indices: 336658--336686 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
336648 GAGGGTATAA
336658 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
336673 TAGTCCTTCGGGAT
1 TAGTCCTTCGGGAT
336687 ATAGGAGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.31, T:0.34
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:339120 original size:55 final size:53
Alignment explanation
Indices: 339060--339228 Score: 186
Period size: 55 Copynumber: 3.2 Consensus size: 53
339050 GTGCTTTTTT
*
339060 AAAGAAACTAAGTCCGATTTTTGGAAGTTTCTTGATTATTTTTAAATGAACTTTC
1 AAAGAAACTAAGT-C-ATTTTTGGAAGTTTCTTGATTATTTTTAAATGAACTTTA
*** * *
339115 AAAGAAACTAAGTCTAATTTTCATAAGTTTCCTGATGA-TTTTAAATGAAC-TTA
1 AAAGAAACTAAGTC--ATTTTTGGAAGTTTCTTGATTATTTTTAAATGAACTTTA
* *
339168 AAAGAAACTAA---ATTTTTGGAAGTTTCTTGATTATTTTTAAATGAATTTTT
1 AAAGAAACTAAGTCATTTTTGGAAGTTTCTTGATTATTTTTAAATGAACTTTA
*
339218 AAAGAAGCTAA
1 AAAGAAACTAA
339229 TCCTAATTCT
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
48 17 0.18
49 11 0.11
50 12 0.12
53 13 0.14
54 13 0.14
55 30 0.31
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (53 bp):
AAAGAAACTAAGTCATTTTTGGAAGTTTCTTGATTATTTTTAAATGAACTTTA
Found at i:339440 original size:84 final size:85
Alignment explanation
Indices: 339338--339505 Score: 284
Period size: 85 Copynumber: 2.0 Consensus size: 85
339328 GCATGATTTG
* *
339338 TAAGTCCTTCGGGTCATCCATAAGACCTTCGGGC-GGATGTTTTCAACATTTCCTTTGCTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTCCTCGATT
*
339402 CACAACACTTCGAATCAGCT
66 CACAACACCTCGAATCAGCT
* *
339422 TAAGTCCTTCGGGCCATCCATAAGATCTTCGGGCATGATGTTTTCAACATTTCCTTTCCTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTCCTCGATT
339487 CACAACACCTCGAATCAGC
66 CACAACACCTCGAATCAGC
339506 AACACCTCAC
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 32 0.41
85 46 0.59
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.32
Consensus pattern (85 bp):
TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTCCTCGATT
CACAACACCTCGAATCAGCT
Found at i:339499 original size:15 final size:16
Alignment explanation
Indices: 339479--339513 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
339469 CATTTCCTTT
*
339479 CCTCGATTCA-CAACA
1 CCTCGAATCAGCAACA
339494 CCTCGAATCAGCAACA
1 CCTCGAATCAGCAACA
339510 CCTC
1 CCTC
339514 ACTAGATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.31, C:0.43, G:0.09, T:0.17
Consensus pattern (16 bp):
CCTCGAATCAGCAACA
Found at i:340739 original size:40 final size:40
Alignment explanation
Indices: 340657--340792 Score: 170
Period size: 39 Copynumber: 3.5 Consensus size: 40
340647 TACAATGGAG
*
340657 AGTTCATAATGAGAAGAACTCA-TCGATAGAAGGAGAAGA
1 AGTTCATAATGAGAAGAACTCATTCGACAGAAGGAGAAGA
*
340696 AGTTCATAATGATAAGAACTCATTCGACAGAAGGAGAAGA
1 AGTTCATAATGAGAAGAACTCATTCGACAGAAGGAGAAGA
* * * * * *
340736 AGTTTATAAAGAGAATAACTCATCCAAC-G-AGAGAGAAGT
1 AGTTCATAATGAGAAGAACTCATTCGACAGAAG-GAGAAGA
340775 AGTTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
340793 TTTGTTCAGC
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
38 2 0.02
39 43 0.52
40 38 0.46
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (40 bp):
AGTTCATAATGAGAAGAACTCATTCGACAGAAGGAGAAGA
Found at i:341151 original size:139 final size:137
Alignment explanation
Indices: 340736--341254 Score: 602
Period size: 139 Copynumber: 3.8 Consensus size: 137
340726 AAGGAGAAGA
* * * * * * *
340736 AGTTTATAAAGAGAATAACTCATCCAACGAGAGAGAAGTAGTTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACTAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * *
340801 GCCTTAGCTCGATTCTTCACATATGGAGTTGAATCAGCAACACCTCGCTCGAGGGATCAAAATTT
66 ACCTTAGCTCGATTCATCACATA-GGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACA-TT
*
340866 CCAATGGAG
129 CCAGTGGAG
* * * *
340875 AGTTCATAATGAGAATAACTTATCCGAC-AGAGTGAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AGTTCATAATGAGAAGAACTCATCCAACTAG-G-GAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * ** *
340939 CGACCTATCA-CTCGATTCATGACAT----TTTGAATCAGTGACACCTCACTTGAGGGATCAACA
64 CAACCT-T-AGCTCGATTCATCACATAGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACA
*
340999 CTTCCAGTTGAG
127 -TTCCAGTGGAG
341011 AGTTCATAATGAGAAGAACTCATCCAACTAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACTAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
341076 ACCTTAGCTCGATTCATCACATACGGAGTTGAATCAGCAATACCTTACTCGAGGGATCAACATTC
66 ACCTTAGCTCGATTCATCACATA-GGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATT-
341141 CCAGTGGAG
129 CCAGTGGAG
* *
341150 AGTTCATAATGAGAAGAATTCATCCGA-TGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCCAACT-AGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
341214 AACCTTAGCTTGTTTCCATCGCATAAGGAGTTGAAACAGCA
65 AACCTTAGCTCGATT-CATCACAT-AGGAGTTGAATCAGCA
341255 CCAACTTTTC
Statistics
Matches: 325, Mismatches: 40, Indels: 29
0.82 0.10 0.07
Matches are distributed among these distances:
133 1 0.00
134 15 0.05
135 35 0.11
136 64 0.20
137 2 0.01
138 5 0.02
139 134 0.41
140 53 0.16
141 15 0.05
142 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (137 bp):
AGTTCATAATGAGAAGAACTCATCCAACTAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTAGCTCGATTCATCACATAGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTCC
AGTGGAG
Found at i:356346 original size:33 final size:33
Alignment explanation
Indices: 356303--356396 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
356293 ACTGATAATG
*
356303 TAATACCCCAAACTTCGGGATAGTAGTTCAATT
1 TAATACCCCAAACTTCGAGATAGTAGTTCAATT
* *
356336 TAATAACCCAAACTTCGAGTTAGTAGTTCAATT
1 TAATACCCCAAACTTCGAGATAGTAGTTCAATT
* * *
356369 TAATACCCCAAACTCCAAGTTAGTAGTT
1 TAATACCCCAAACTTCGAGATAGTAGTT
356397 TGGGTTGACC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (33 bp):
TAATACCCCAAACTTCGAGATAGTAGTTCAATT
Found at i:366171 original size:18 final size:20
Alignment explanation
Indices: 366101--366172 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
366091 TGGATAAGGT
*
366101 AGTATCAATACTCT-AGGCTG
1 AGTATCGATACTCTGA-GCTG
366121 AGTATCGATACTCTGATGCTG
1 AGTATCGATACTCTGA-GCTG
*
366142 AGGTATCAATACT-TGA-CTG
1 A-GTATCGATACTCTGAGCTG
366161 AGTATCGATACT
1 AGTATCGATACT
366173 AAATTTAGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.22
19 4 0.09
20 13 0.28
21 9 0.20
22 10 0.22
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTATCGATACTCTGAGCTG
Found at i:370052 original size:20 final size:21
Alignment explanation
Indices: 369997--370054 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 21
369987 CTCAGCAGTG
369997 AAGGGATCGATCCTTTTTTAA
1 AAGGGATCGATCCTTTTTTAA
* *
370018 AAGGGGTCGGT-CTTTTTT-A
1 AAGGGATCGATCCTTTTTTAA
*
370037 GAGGGATCGATCCTTTTT
1 AAGGGATCGATCCTTTTT
370055 CATGGGGATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 9 0.29
20 13 0.42
21 9 0.29
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.40
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTTTAA
Found at i:370120 original size:21 final size:21
Alignment explanation
Indices: 370090--370140 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
370080 AGTAAGTTTG
*
370090 GGATCAATCCTTCAAGCCAAT
1 GGATCGATCCTTCAAGCCAAT
370111 GGATCGATCCTTCAAGCCAAT
1 GGATCGATCCTTCAAGCCAAT
370132 GGATCGATC
1 GGATCGATC
370141 ATTTTCCCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
GGATCGATCCTTCAAGCCAAT
Found at i:372224 original size:19 final size:19
Alignment explanation
Indices: 372200--372241 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
372190 ATCTCAATAA
*
372200 TTAACTC-CGAAAATCATTT
1 TTAACTCAC-AAAATCAATT
372219 TTAACTCACAAAATCAATT
1 TTAACTCACAAAATCAATT
372238 TTAA
1 TTAA
372242 TATATTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (19 bp):
TTAACTCACAAAATCAATT
Found at i:378982 original size:328 final size:328
Alignment explanation
Indices: 378378--379041 Score: 1292
Period size: 328 Copynumber: 2.0 Consensus size: 328
378368 TTACTTTAAG
*
378378 AAAATTTAATATTTGTTCGTATAACCTTTTATTTTTTGGATTTTTTTTCTAATTCAAGTCATAAT
1 AAAATTGAATATTTGTTCGTATAACCTTTTATTTTTTGGATTTTTTTTCTAATTCAAGTCATAAT
378443 GCTGCAATTAAATCCATGCGCCACTCACGGCGGACGGTTTTGACAGCTGATGGCGTTGACAGTGC
66 GCTGCAATTAAATCCATGCGCCACTCACGGCGGACGGTTTTGACAGCTGATGGCGTTGACAGTGC
378508 TCCTAATCTGCGAAACTTGGAGGTATATTTTAAGTTCTAATAATTTTTGTTCTGCTTATTGTAAA
131 TCCTAATCTGCGAAACTTGGAGGTATATTTTAAGTTCTAATAATTTTTGTTCTGCTTATTGTAAA
378573 TTTCTTACATATATATTTTCTTTTGTTAGTTGAGAATAGTACTAATTAATGTTACTACTTAGTAT
196 TTTCTTACATATATATTTTCTTTTGTTAGTTGAGAATAGTACTAATTAATGTTACTACTTAGTAT
378638 AATTTTGTAGGAATTTATGAATTTTTGAAGTGATGTCATAATTTCTAGGTCATGTGTACTAAACC
261 AATTTTGTAGGAATTTATGAATTTTTGAAGTGATGTCATAATTTCTAGGTCATGTGTACTAAACC
378703 AAT
326 AAT
378706 AAAATTGAATATTTGTTCGTATAACCTTTTATTTTTTGGATTTTTTTTCTAATTCAAGTCATAAT
1 AAAATTGAATATTTGTTCGTATAACCTTTTATTTTTTGGATTTTTTTTCTAATTCAAGTCATAAT
*
378771 GCTGCAATTAAATCCATGTGCCACTCACGGCGGACGGTTTTGACAGCTGATGGCGTTGACAGTGC
66 GCTGCAATTAAATCCATGCGCCACTCACGGCGGACGGTTTTGACAGCTGATGGCGTTGACAGTGC
378836 TCCTAATCTGCGAAACTTGGAGGTATATTTTAAGTTCTAATAATTTTTGTTCTGCTTATTGTAAA
131 TCCTAATCTGCGAAACTTGGAGGTATATTTTAAGTTCTAATAATTTTTGTTCTGCTTATTGTAAA
*
378901 TTTCTTACATATATATTTTCTTTTGTTAGTTGAGAATAGTACTAATTAATGTTACTTCTTAGTAT
196 TTTCTTACATATATATTTTCTTTTGTTAGTTGAGAATAGTACTAATTAATGTTACTACTTAGTAT
378966 AATTTTGTAGGAATTTATGAATTTTTGAAGTGATGTCATAATTTCTAGGTCATGTGTACTAAACC
261 AATTTTGTAGGAATTTATGAATTTTTGAAGTGATGTCATAATTTCTAGGTCATGTGTACTAAACC
*
379031 CAT
326 AAT
379034 AAAATTGA
1 AAAATTGA
379042 CCAAAAGTGG
Statistics
Matches: 332, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
328 332 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (328 bp):
AAAATTGAATATTTGTTCGTATAACCTTTTATTTTTTGGATTTTTTTTCTAATTCAAGTCATAAT
GCTGCAATTAAATCCATGCGCCACTCACGGCGGACGGTTTTGACAGCTGATGGCGTTGACAGTGC
TCCTAATCTGCGAAACTTGGAGGTATATTTTAAGTTCTAATAATTTTTGTTCTGCTTATTGTAAA
TTTCTTACATATATATTTTCTTTTGTTAGTTGAGAATAGTACTAATTAATGTTACTACTTAGTAT
AATTTTGTAGGAATTTATGAATTTTTGAAGTGATGTCATAATTTCTAGGTCATGTGTACTAAACC
AAT
Found at i:384568 original size:51 final size:51
Alignment explanation
Indices: 384513--384628 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
384503 GTCAATCTTA
* *
384513 TCATGGAACTGAGGTGATGGTGGAATATTACTAGAATGCTGGTTATTTGCT
1 TCATGGAACTGAGGTGATGGTGGAATATCACTAGAATGCAGGTTATTTGCT
* *
384564 TCATGGAAATGAGGTGGTGGTGGAATATCACTAGAATGCAGGTTATTTGCT
1 TCATGGAACTGAGGTGATGGTGGAATATCACTAGAATGCAGGTTATTTGCT
*
384615 TCATGGAACCGAGG
1 TCATGGAACTGAGG
384629 AAATGGATCG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.31
Consensus pattern (51 bp):
TCATGGAACTGAGGTGATGGTGGAATATCACTAGAATGCAGGTTATTTGCT
Found at i:392625 original size:147 final size:147
Alignment explanation
Indices: 392358--392654 Score: 594
Period size: 147 Copynumber: 2.0 Consensus size: 147
392348 GTAAAATAAA
392358 TGACATGAAGAAACAGTGAAAACACCAAGAACTCTAAAATTATGAATTAACCACCAAAATCTTGC
1 TGACATGAAGAAACAGTGAAAACACCAAGAACTCTAAAATTATGAATTAACCACCAAAATCTTGC
392423 TCTTGAATTAGGCTCTTGAGATTCAGTGACCTTTACATCAGCCGGGAGCTTATCTTTTTTGGATT
66 TCTTGAATTAGGCTCTTGAGATTCAGTGACCTTTACATCAGCCGGGAGCTTATCTTTTTTGGATT
392488 TGGAAGTCAGAAGGAGC
131 TGGAAGTCAGAAGGAGC
392505 TGACATGAAGAAACAGTGAAAACACCAAGAACTCTAAAATTATGAATTAACCACCAAAATCTTGC
1 TGACATGAAGAAACAGTGAAAACACCAAGAACTCTAAAATTATGAATTAACCACCAAAATCTTGC
392570 TCTTGAATTAGGCTCTTGAGATTCAGTGACCTTTACATCAGCCGGGAGCTTATCTTTTTTGGATT
66 TCTTGAATTAGGCTCTTGAGATTCAGTGACCTTTACATCAGCCGGGAGCTTATCTTTTTTGGATT
392635 TGGAAGTCAGAAGGAGC
131 TGGAAGTCAGAAGGAGC
392652 TGA
1 TGA
392655 TGAAGCCTTA
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 150 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (147 bp):
TGACATGAAGAAACAGTGAAAACACCAAGAACTCTAAAATTATGAATTAACCACCAAAATCTTGC
TCTTGAATTAGGCTCTTGAGATTCAGTGACCTTTACATCAGCCGGGAGCTTATCTTTTTTGGATT
TGGAAGTCAGAAGGAGC
Done.