Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005203.1 Hibiscus syriacus cultivar Beakdansim tig00011761_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: 1490345
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1316249 original size:86 final size:87
Alignment explanation
Indices: 1316086--1316255 Score: 208
Period size: 88 Copynumber: 2.0 Consensus size: 87
1316076 TTAATTTTTA
*
1316086 TTTTTTACCTTTATAATTGAAGTCCTAATATTATTCAATCTCACCTTTTATCTTTATAATTGAAG
1 TTTTTTACCTTTATAATTGAACTCCTAATATTATTCAATCTCACCTTTTATCTTTATAATTGAAG
*
1316151 TCTCTAATTTTTTTTCAATCCCT
66 TCTCTAA-GTTTTTTCAATCCCT
*
1316174 TTTTTTACCTTTATAATTGAGACTCCTAAT-TT-TGT-AATCTTA-CTTTTAAT-TTTATAATTG
1 TTTTTTACCTTTATAATTGA-ACTCCTAATATTAT-TCAATCTCACCTTTT-ATCTTTATAATTG
* *
1316234 ATG-CTTTTAAGTTTTTTCAATC
63 AAGTC-TCTAAGTTTTTTCAATC
1316256 TCAATTTCCA
Statistics
Matches: 73, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
85 12 0.16
86 21 0.29
87 9 0.12
88 23 0.32
89 8 0.11
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (87 bp):
TTTTTTACCTTTATAATTGAACTCCTAATATTATTCAATCTCACCTTTTATCTTTATAATTGAAG
TCTCTAAGTTTTTTCAATCCCT
Found at i:1316381 original size:46 final size:45
Alignment explanation
Indices: 1316325--1316509 Score: 158
Period size: 45 Copynumber: 4.2 Consensus size: 45
1316315 TTTAGACCCT
1316325 TAAGTTTTTTTTAATCTCACTTTCCACCTTTTCAATTGAGGCCCC
1 TAAGTTTTTTTTAATCTCACTTTCCACCTTTTCAATTGAGGCCCC
* *
1316370 TAAGTTTTTTTTCAATCTCAATTTCCA-CTTTTATAATTGAGGCCCC
1 TAAGTTTTTTTT-AATCTCACTTTCCACCTTTT-CAATTGAGGCCCC
* ** * *
1316416 -----TTTTTTTAATCCCACTTTTTTAACCTTATT--ATTTAGGCCCT
1 TAAGTTTTTTTTAATCTCAC--TTTCCACCTT-TTCAATTGAGGCCCC
* *
1316457 TAAG-TTTTTTTAATCTCAC-TTCTAAC-TTTCTAATTGAGGCCCC
1 TAAGTTTTTTTTAATCTCACTTTCCACCTTTTC-AATTGAGGCCCC
1316500 TAAGTTTTTT
1 TAAGTTTTTT
1316510 CGATCTCAAT
Statistics
Matches: 112, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
40 8 0.07
41 17 0.15
42 8 0.07
43 16 0.14
44 7 0.06
45 31 0.28
46 25 0.22
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.48
Consensus pattern (45 bp):
TAAGTTTTTTTTAATCTCACTTTCCACCTTTTCAATTGAGGCCCC
Found at i:1316398 original size:131 final size:128
Alignment explanation
Indices: 1316241--1316554 Score: 474
Period size: 131 Copynumber: 2.4 Consensus size: 128
1316231 TTGATGCTTT
*
1316241 TAAGTTTTTTCAATCTCAATTTCCACTTTTATAATTGAGACCCCTTTTTTTAATCCCAC-TTTTT
1 TAAGTTTTTTCAATCTCAATTTCCACTTTTATAATTGAGGCCCCTTTTTTTAATCCCACTTTTTT
*
1316305 AACCTTATTATTTAGACCCTTAAGTTTTTTTTAATCTCACTTTCCACCTTT-TCAATTGAGGCCC
66 AACCTTATTATTTAGACCCTTAAG-TTTTTTTAATCTCAC-TTCCAACTTTCT-AATTGAGGCCC
1316369 C
128 C
1316370 TAAGTTTTTTTTCAATCTCAATTTCCACTTTTATAATTGAGGCCCCTTTTTTTAATCCCACTTTT
1 TAAG--TTTTTTCAATCTCAATTTCCACTTTTATAATTGAGGCCCCTTTTTTTAATCCCACTTTT
* *
1316435 TTAACCTTATTATTTAGGCCCTTAAGTTTTTTTAATCTCACTTCTAACTTTCTAATTGAGGCCCC
64 TTAACCTTATTATTTAGACCCTTAAGTTTTTTTAATCTCACTTCCAACTTTCTAATTGAGGCCCC
* * *
1316500 TAAGTTTTTTCGATCTCAATTAT--ACCTTTATAATTGAGGCCCTTATTTTTTAATC
1 TAAGTTTTTTCAATCTCAATT-TCCACTTTTATAATTGAGGCCCCT-TTTTTTAATC
1316555 GATTTCTACC
Statistics
Matches: 172, Mismatches: 7, Indels: 13
0.90 0.04 0.07
Matches are distributed among these distances:
127 19 0.11
128 26 0.15
129 5 0.03
130 24 0.14
131 70 0.41
132 28 0.16
ACGTcount: A:0.23, C:0.22, G:0.07, T:0.47
Consensus pattern (128 bp):
TAAGTTTTTTCAATCTCAATTTCCACTTTTATAATTGAGGCCCCTTTTTTTAATCCCACTTTTTT
AACCTTATTATTTAGACCCTTAAGTTTTTTTAATCTCACTTCCAACTTTCTAATTGAGGCCCC
Found at i:1316498 original size:43 final size:43
Alignment explanation
Indices: 1316182--1316592 Score: 187
Period size: 43 Copynumber: 9.7 Consensus size: 43
1316172 CTTTTTTTAC
* * * *
1316182 CTTTATAATTGAGACTCC-TAA--TTTTGTAATCTTACTTTTAA
1 CTTTATAATTGAGGC-CCTTAAGTTTTTTTAATCTCACTTCTAA
* * ** * * *
1316223 TTTTATAATTGATGCTTTTAAGTTTTTTCAATCTCAATT-TCCA
1 CTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTCT-AA
* * * *
1316266 CTTTTATAATTGAGACCC----CTTTTTTTAATCCCACTTTTTAA
1 C-TTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCAC-TTCTAA
* * * * * *
1316307 CCTTATTATTTAGACCCTTAAGTTTTTTTTAATCTCACTTTCCAC
1 CTTTATAATTGAGGCCCTTAAG-TTTTTTTAATCTCAC-TTCTAA
* * *
1316352 CTTT-TCAATTGAGGCCCCTAAGTTTTTTTTCAATCTCAATT-TCCA
1 CTTTAT-AATTGAGGCCCTTAAG-TTTTTTT-AATCTCACTTCT-AA
* * *
1316397 CTTTTATAATTGAGGCCC----CTTTTTTTAATCCCACTTTTTTAA
1 C-TTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCAC--TTCTAA
* * *
1316439 CCTTATTATTTAGGCCCTTAAGTTTTTTTAATCTCACTTCTAA
1 CTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTCTAA
* * ** * * *
1316482 CTTTCTAATTGAGGCCCCTAAGTTTTTTCGATCTCAATTATAC
1 CTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTCTAA
* * *
1316525 CTTTATAATTGAGGCCCTT-A--TTTTTTAATC-GATTTCTAC
1 CTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTCTAA
*
1316564 CTTTATAATTAAGG-CCTCTAA-TTTTTTTA
1 CTTTATAATTGAGGCCCT-TAAGTTTTTTTA
1316593 CAATTTTATA
Statistics
Matches: 278, Mismatches: 65, Indels: 54
0.70 0.16 0.14
Matches are distributed among these distances:
38 3 0.01
39 20 0.07
40 40 0.14
41 46 0.17
42 7 0.03
43 69 0.25
44 13 0.05
45 58 0.21
46 21 0.08
47 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (43 bp):
CTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTCTAA
Found at i:1322892 original size:60 final size:60
Alignment explanation
Indices: 1322821--1322944 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 60
1322811 TCAGATAACT
*
1322821 ATTTTGTAACTTTTAATAG-TCAATGGACTCAACAAAGCAATATCCTATAGTCGGAGGATCC
1 ATTTTGTAACTTTTAATAGTTCAA-GGACTCAACAAAGCAACATCCTATAGTCGGAGGA-CC
* * * *
1322882 ATTTT-TAACTTTTGATAGTTGAAGGACTCAACAAAGCAACATTCTATAGTCGGAGTACC
1 ATTTTGTAACTTTTAATAGTTCAAGGACTCAACAAAGCAACATCCTATAGTCGGAGGACC
1322941 ATTT
1 ATTT
1322945 GTATATTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
59 6 0.11
60 43 0.75
61 8 0.14
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTTCAAGGACTCAACAAAGCAACATCCTATAGTCGGAGGACC
Found at i:1336290 original size:41 final size:40
Alignment explanation
Indices: 1336245--1336322 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 40
1336235 TCACTGTGAT
*
1336245 AGTTTGTGTTGTGAAATTCGTTACACACGTTTTCATATCAC
1 AGTTTGTGTTGTGAAATTCGTTAAACACG-TTTCATATCAC
* *
1336286 AGTTTGTGTTGTGAAATTTGTTAAACATGTTTCATAT
1 AGTTTGTGTTGTGAAATTCGTTAAACACGTTTCATAT
1336323 GTATTTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 8 0.24
41 26 0.76
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.45
Consensus pattern (40 bp):
AGTTTGTGTTGTGAAATTCGTTAAACACGTTTCATATCAC
Found at i:1340374 original size:18 final size:19
Alignment explanation
Indices: 1340347--1340388 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1340337 TAAATAATTT
1340347 ATTT-AAAT-AACGTTAAC
1 ATTTAAAATAAACGTTAAC
*
1340364 ATTTAAAATAAATGTTAAC
1 ATTTAAAATAAACGTTAAC
*
1340383 GTTTAA
1 ATTTAA
1340389 TTTATTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 4 0.19
19 13 0.62
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (19 bp):
ATTTAAAATAAACGTTAAC
Found at i:1351202 original size:23 final size:21
Alignment explanation
Indices: 1351170--1351229 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1351160 TTGGTGCAGA
1351170 GGGAATCGATACCCCCTTTGAAG
1 GGGAATCGATACCCCC--TGAAG
* * *
1351193 GGGAACCGATTCCCCCTGTAG
1 GGGAATCGATACCCCCTGAAG
1351214 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
1351230 CTGGGGTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 18 0.56
23 14 0.44
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (21 bp):
GGGAATCGATACCCCCTGAAG
Found at i:1353792 original size:21 final size:21
Alignment explanation
Indices: 1353759--1353800 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1353749 TCCAGTATGT
1353759 CCAGAGGGAACCGATTCCCCC
1 CCAGAGGGAACCGATTCCCCC
* *
1353780 CCAGGGGGTACCGATTCCCCC
1 CCAGAGGGAACCGATTCCCCC
1353801 TTGAATGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.43, G:0.26, T:0.12
Consensus pattern (21 bp):
CCAGAGGGAACCGATTCCCCC
Found at i:1361028 original size:19 final size:19
Alignment explanation
Indices: 1360998--1361050 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
1360988 TGAATAACTA
1360998 AATAATATAATATAATAAAT
1 AATAA-ATAATATAATAAAT
1361018 AATAAATAATAGT-ATAAAT
1 AATAAATAATA-TAATAAAT
*
1361037 AATATATAATATAA
1 AATAAATAATATAA
1361051 CATGTAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 23 0.77
20 6 0.20
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AATAAATAATATAATAAAT
Found at i:1361050 original size:12 final size:12
Alignment explanation
Indices: 1361002--1361050 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
1360992 TAACTAAATA
1361002 ATATAATATAAT
1 ATATAATATAAT
*
1361014 AAATAATAAATAAT
1 ATATAAT--ATAAT
1361028 AGTATAA-ATAAT
1 A-TATAATATAAT
1361040 ATATAATATAA
1 ATATAATATAA
1361051 CATGTAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
11 5 0.16
12 16 0.52
14 6 0.19
15 4 0.13
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
ATATAATATAAT
Found at i:1361121 original size:26 final size:27
Alignment explanation
Indices: 1361092--1361146 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1361082 CAAAAACTAT
*
1361092 ACATATGTTTTC-AAAACGTTTTCAAA
1 ACATACGTTTTCAAAAACGTTTTCAAA
*
1361118 ACATACGTTTTCAAAAATGTTTTCAAA
1 ACATACGTTTTCAAAAACGTTTTCAAA
1361145 AC
1 AC
1361147 CATTATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.36
Consensus pattern (27 bp):
ACATACGTTTTCAAAAACGTTTTCAAA
Found at i:1361127 original size:15 final size:15
Alignment explanation
Indices: 1361107--1361146 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1361097 TGTTTTCAAA
1361107 ACGTTTTCAAAACAT
1 ACGTTTTCAAAACAT
1361122 ACGTTTTCAAAA-AT
1 ACGTTTTCAAAACAT
1361136 --GTTTTCAAAAC
1 ACGTTTTCAAAAC
1361147 CATTATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.42
14 2 0.08
15 12 0.50
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (15 bp):
ACGTTTTCAAAACAT
Found at i:1361201 original size:35 final size:34
Alignment explanation
Indices: 1361124--1361359 Score: 179
Period size: 38 Copynumber: 6.6 Consensus size: 34
1361114 CAAAACATAC
* * *
1361124 GTTTTCAAAAATGTTTTCAAAACCATTATATTATATAT
1 GTTTTCAAAACT-TTTTTAAAACTA-TATA-T-TATAT
* *
1361162 GTTTTCAAAACCTTTTTTAAAATTATATATTATAC
1 GTTTTCAAAA-CTTTTTTAAAACTATATATTATAT
* *
1361197 GTTTTCGAAACTGTTTTAAAA-TATATATTATAT
1 GTTTTCAAAACTTTTTTAAAACTATATATTATAT
* * *
1361230 ATTTTCGAAACTATTTTAAAAACTATATATTATACAT
1 GTTTTCAAAACT-TTTTTAAAACTATATATTAT--AT
* * * *
1361267 -TTTTAAAATTATTTTTTTAAAAACTGTATACTATAT
1 GTTTTCAAA--ACTTTTTT-AAAACTATATATTATAT
* *
1361303 GATTTTCAAAACCGTTTTAAAAACTATATATTATAT
1 G-TTTTCAAAA-CTTTTTTAAAACTATATATTATAT
* *
1361339 GCTTTCAAAACTATTTTAAAA
1 GTTTTCAAAACTTTTTTAAAA
1361360 AAAAGTATAT
Statistics
Matches: 160, Mismatches: 27, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
33 22 0.14
34 25 0.16
35 31 0.19
36 26 0.16
37 14 0.09
38 41 0.26
39 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (34 bp):
GTTTTCAAAACTTTTTTAAAACTATATATTATAT
Found at i:1361360 original size:35 final size:35
Alignment explanation
Indices: 1361124--1361417 Score: 209
Period size: 35 Copynumber: 8.1 Consensus size: 35
1361114 CAAAACATAC
* * * *
1361124 GTTTTCAAAAATGTTTTCAAAACCATTATATTATATAT
1 GTTTTCAAAACTATTTTAAAAACTA-TATA-T-TATAT
* * *
1361162 GTTTTCAAAACCT-TTTTTAAAATTATATATTATAC
1 GTTTTCAAAA-CTATTTTAAAAACTATATATTATAT
* *
1361197 GTTTTCGAAACTGTTTT-AAAA-TATATATTATAT
1 GTTTTCAAAACTATTTTAAAAACTATATATTATAT
* * *
1361230 ATTTTCGAAACTATTTTAAAAACTATATATTATAC
1 GTTTTCAAAACTATTTTAAAAACTATATATTATAT
* * * * *
1361265 ATTTTTAAAATTATTTTTTTAAAAACTGTATACTATAT
1 GTTTTCAAAACTA---TTTTAAAAACTATATATTATAT
**
1361303 GATTTTCAAAACCGTTTTAAAAACTATATATTATAT
1 G-TTTTCAAAACTATTTTAAAAACTATATATTATAT
* **
1361339 GCTTTCAAAACTATTTTAAAAAAAAGTATATATATAT
1 GTTTTCAAAACTATTTTAAAAACTA-TATAT-TATAT
* ** *
1361376 TTTTTTTAAA-TAAGTTTTCAAAAACGATATATTATAT
1 GTTTTCAAAACT-A-TTTT-AAAAACTATATATTATAT
1361413 GTTTT
1 GTTTT
1361418 GAAATTATTA
Statistics
Matches: 208, Mismatches: 35, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
33 26 0.12
34 10 0.05
35 57 0.27
36 28 0.13
37 25 0.12
38 47 0.23
39 15 0.07
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (35 bp):
GTTTTCAAAACTATTTTAAAAACTATATATTATAT
Found at i:1361363 original size:74 final size:69
Alignment explanation
Indices: 1361120--1361378 Score: 220
Period size: 68 Copynumber: 3.6 Consensus size: 69
1361110 TTTTCAAAAC
* * * *
1361120 ATACGTTTTCAAAAATGTTTTCAAAACCATTATATTATATATG-TTTTCAAAACCTTTTTTAAAA
1 ATACGTTTTCAAAACTATTTT-AAAA--A-TATA-TATATATGATTTTCAAAACCGTTTTAAAAA
*
1361184 TTATATATT
61 CTATATATT
* * * **
1361193 ATACGTTTTCGAAACTGTTTT-AAAATATATATTATAT-ATTTTCGAAACTATTTTAAAAACTAT
1 ATACGTTTTCAAAACTATTTTAAAAATATATA-TATATGATTTTCAAAACCGTTTTAAAAACTAT
1361256 ATATT
65 ATATT
* * * *
1361261 ATACATTTTTAAAATTATTTTTTTAAAAACTGTATACTATATGATTTTCAAAACCGTTTTAAAAA
1 ATACGTTTTCAAAACTA---TTTTAAAAA-TATATA-TATATGATTTTCAAAACCGTTTTAAAAA
1361326 CTATATATT
61 CTATATATT
* * *
1361335 ATATGCTTTCAAAACTATTTTAAAAAAAAGTATATATAT-ATTTT
1 ATACGTTTTCAAAACTATTTT-AAAAATA-TATATATATGATTTT
1361379 TTTTAAATAA
Statistics
Matches: 152, Mismatches: 24, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
67 2 0.01
68 46 0.30
69 1 0.01
70 5 0.03
71 16 0.11
72 13 0.09
73 29 0.19
74 40 0.26
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.46
Consensus pattern (69 bp):
ATACGTTTTCAAAACTATTTTAAAAATATATATATATGATTTTCAAAACCGTTTTAAAAACTATA
TATT
Found at i:1363000 original size:21 final size:20
Alignment explanation
Indices: 1362966--1363039 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
1362956 TAAGGAATAG
*
1362966 TATCT-TTTAGGATTTCTTTT
1 TATCTATTTAAGA-TTCTTTT
1362986 TATCTATTTAAGATT-TTTT
1 TATCTATTTAAGATTCTTTT
1363005 TA--TA--TAA-ATTCTCTTT
1 TATCTATTTAAGATTCT-TTT
1363021 TATCTATTTAAGATT-TTTT
1 TATCTATTTAAGATTCTTTT
1363040 GAATAGTCGG
Statistics
Matches: 45, Mismatches: 1, Indels: 17
0.71 0.02 0.27
Matches are distributed among these distances:
14 3 0.07
15 4 0.09
16 5 0.11
17 2 0.04
18 2 0.04
19 9 0.20
20 11 0.24
21 9 0.20
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.62
Consensus pattern (20 bp):
TATCTATTTAAGATTCTTTT
Found at i:1363006 original size:19 final size:19
Alignment explanation
Indices: 1362982--1363039 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
1362972 TTAGGATTTC
1362982 TTTTTATCTATTTAAGATT
1 TTTTTATCTATTTAAGATT
1363001 TTTTTA--TA--TAA-ATT
1 TTTTTATCTATTTAAGATT
1363015 CTCTTTTATCTATTTAAGATT
1 -T-TTTTATCTATTTAAGATT
1363036 TTTT
1 TTTT
1363040 GAATAGTCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 5 0.16
17 2 0.06
18 2 0.06
19 9 0.28
20 4 0.12
21 3 0.09
ACGTcount: A:0.26, C:0.07, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTATCTATTTAAGATT
Found at i:1375802 original size:76 final size:74
Alignment explanation
Indices: 1375676--1375836 Score: 200
Period size: 76 Copynumber: 2.1 Consensus size: 74
1375666 AGCATATATG
* * * *
1375676 AATATGATTTACAATATTTTTTATATTTATTAATTCTTGTTAATGGAAGAAATA-ATTCTTATTT
1 AATAT-ATTTAAAATATTTTTTATATTTATAAATTCTTGTTAATGAAAGAAA-AGATTCTTAATT
* *
1375740 TTTATTTATTA
64 TGTATTTAATA
*
1375751 AATATAATTTAAAATAATTTTTTTATATTT-TAAATTTTTGTTAATGAAAGAAAAGATTCTTAAT
1 AATAT-ATTTAAAAT-A-TTTTTTATATTTATAAATTCTTGTTAATGAAAGAAAAGATTCTTAAT
1375815 TTGTATTTAATA
63 TTGTATTTAATA
1375827 AATATATTTA
1 AATATATTTA
1375837 TTAATATGTA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
75 19 0.25
76 44 0.59
77 12 0.16
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.52
Consensus pattern (74 bp):
AATATATTTAAAATATTTTTTATATTTATAAATTCTTGTTAATGAAAGAAAAGATTCTTAATTTG
TATTTAATA
Found at i:1375850 original size:14 final size:14
Alignment explanation
Indices: 1375810--1375854 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1375800 GAAAAGATTC
*
1375810 TTAATTTGTATTTA
1 TTAATATGTATTTA
* *
1375824 ATAA-ATATATTTA
1 TTAATATGTATTTA
1375837 TTAATATGTATTTA
1 TTAATATGTATTTA
1375851 TTAA
1 TTAA
1375855 ATTTTTATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (14 bp):
TTAATATGTATTTA
Found at i:1383043 original size:18 final size:19
Alignment explanation
Indices: 1383020--1383061 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1383010 GTAAGAAAAT
*
1383020 ATTAAAATAA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
1383038 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAAGTAAAAGCA
1383056 ATTAAA
1 ATTAAA
1383062 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Found at i:1390746 original size:29 final size:29
Alignment explanation
Indices: 1390712--1390770 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1390702 CCTAAATTAA
*
1390712 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGACATTGCTTACATCAATTTAGT
1390741 TTTGATGACATTGCTTACATCAATTTAGT
1 TTTGATGACATTGCTTACATCAATTTAGT
1390770 T
1 T
1390771 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
TTTGATGACATTGCTTACATCAATTTAGT
Found at i:1392866 original size:22 final size:22
Alignment explanation
Indices: 1392841--1392911 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
1392831 ATTAATCTAT
*
1392841 ATATATATATAGATAAACTAAA
1 ATATAAATATAGATAAACTAAA
1392863 ATATAAATATAGATAAACTAAA
1 ATATAAATATAGATAAACTAAA
* *
1392885 ATATAAATATAAATATAC-AAA
1 ATATAAATATAGATAAACTAAA
1392906 AT-TAAA
1 ATATAAA
1392912 ATACCAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 4 0.09
21 5 0.11
22 37 0.80
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (22 bp):
ATATAAATATAGATAAACTAAA
Found at i:1392870 original size:6 final size:6
Alignment explanation
Indices: 1392839--1392901 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
1392829 TAATTAATCT
* * * * *
1392839 ATATAT ATATAT AGATAA ACTA-AA ATATAA ATATAG ATA-AA CTA-AA
1 ATATAA ATATAA ATATAA A-TATAA ATATAA ATATAA ATATAA ATATAA
1392885 ATATAA ATATAA ATATA
1 ATATAA ATATAA ATATA
1392902 CAAAATTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 9 0.19
6 37 0.79
7 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:1392892 original size:28 final size:27
Alignment explanation
Indices: 1392861--1392914 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
1392851 AGATAAACTA
*
1392861 AAATATAAATATAGATAAACTAAAATAT
1 AAATATAAATATACA-AAACTAAAATAT
*
1392889 AAATATAAATATACAAAATTAAAATA
1 AAATATAAATATACAAAACTAAAATA
1392915 CCAAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (27 bp):
AAATATAAATATACAAAACTAAAATAT
Found at i:1392919 original size:14 final size:13
Alignment explanation
Indices: 1392889--1392928 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
1392879 ACTAAAATAT
*
1392889 AAATATAAATATACA
1 AAAT-TAAA-ATACC
1392904 AAATTAAAATACC
1 AAATTAAAATACC
1392917 AAATTAAAATAC
1 AAATTAAAATAC
1392929 GAATAAACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 16 0.67
14 4 0.17
15 4 0.17
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATTAAAATACC
Found at i:1392920 original size:28 final size:28
Alignment explanation
Indices: 1392861--1392928 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
1392851 AGATAAACTA
* *
1392861 AAATATAAATATAGATAAACTAAAATAT
1 AAATATAAATATACATAAACTAAAATAC
*
1392889 AAATATAAATATACA-AAATTAAAATACC
1 AAATATAAATATACATAAACTAAAATA-C
1392917 AAAT-TAAA-ATAC
1 AAATATAAATATAC
1392929 GAATAAACCT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 4 0.11
27 14 0.39
28 18 0.50
ACGTcount: A:0.65, C:0.07, G:0.01, T:0.26
Consensus pattern (28 bp):
AAATATAAATATACATAAACTAAAATAC
Found at i:1393486 original size:6 final size:6
Alignment explanation
Indices: 1393479--1393513 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1393469 GTTCTCTCTG
*
1393479 TTGTTG TTGTTC TTGTTC TTGTTC TTGTTC TTGTT
1 TTGTTC TTGTTC TTGTTC TTGTTC TTGTTC TTGTT
1393514 TGTAGGTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.11, G:0.20, T:0.69
Consensus pattern (6 bp):
TTGTTC
Found at i:1394041 original size:11 final size:12
Alignment explanation
Indices: 1394002--1394060 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 12
1393992 GTAAATGCAA
*
1394002 ATATAATATAAC
1 ATATAATATAAT
*
1394014 A-AT-ATATTAT
1 ATATAATATAAT
1394024 ATATAATA-AAT
1 ATATAATATAAT
*
1394035 ATGTAATATAAT
1 ATATAATATAAT
1394047 AATAATAATATAAT
1 -AT-ATAATATAAT
1394061 TAATAATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
10 6 0.16
11 13 0.35
12 7 0.19
13 2 0.05
14 9 0.24
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (12 bp):
ATATAATATAAT
Found at i:1394053 original size:18 final size:17
Alignment explanation
Indices: 1394001--1394069 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 17
1393991 TGTAAATGCA
*
1394001 AATA-TAATATAACAAT
1 AATATTAATATAATAAT
1394017 -ATATT-ATAT-ATAAT
1 AATATTAATATAATAAT
1394031 AAATATGTAATATAATAAT
1 -AATAT-TAATATAATAAT
1394050 AATAATATAAT-TAATAAT
1 AAT-AT-TAATATAATAAT
1394068 AA
1 AA
1394070 AAACGGACAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
14 4 0.09
15 7 0.16
16 5 0.11
17 1 0.02
18 16 0.36
19 11 0.25
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (17 bp):
AATATTAATATAATAAT
Found at i:1394064 original size:12 final size:13
Alignment explanation
Indices: 1394001--1394068 Score: 70
Period size: 13 Copynumber: 5.3 Consensus size: 13
1393991 TGTAAATGCA
*
1394001 AATATAATATAAC
1 AATATAATATAAT
*
1394014 AATATATTATATAT
1 AATATAATATA-AT
*
1394028 AATA-AATAT-GT
1 AATATAATATAAT
1394039 AATATAATAATAAT
1 AATATAAT-ATAAT
1394053 AATATAAT-TAAT
1 AATATAATATAAT
1394065 AATA
1 AATA
1394069 AAAACGGACA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
11 5 0.11
12 11 0.24
13 16 0.35
14 14 0.30
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (13 bp):
AATATAATATAAT
Found at i:1394355 original size:20 final size:20
Alignment explanation
Indices: 1394283--1394356 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
1394273 TCATTTGGCT
* *
1394283 CGAAAGATTGATAGATGACC
1 CGAAAGATTTACAGATGACC
* *
1394303 CGAAGGATTTAACATCATG-CC
1 CGAAAGATTT-ACA-GATGACC
* *
1394324 CGAAAGACTTACAGATGACT
1 CGAAAGATTTACAGATGACC
*
1394344 CGAAGGATTTACA
1 CGAAAGATTTACA
1394357 AATTCATGGT
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (20 bp):
CGAAAGATTTACAGATGACC
Found at i:1394557 original size:41 final size:41
Alignment explanation
Indices: 1394512--1394598 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
1394502 GGATGGCCTT
* *
1394512 AAGGACTTATCATC-TAGCTTGAAAGACTAACAGATAACCCG
1 AAGGACTTAACATCAT-GCTCGAAAGACTAACAGATAACCCG
* * * *
1394553 AAGGATTTAACATCATGCTCGAAAGACTTACATATGACCCG
1 AAGGACTTAACATCATGCTCGAAAGACTAACAGATAACCCG
1394594 AAGGA
1 AAGGA
1394599 TTTACAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 38 0.97
42 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (41 bp):
AAGGACTTAACATCATGCTCGAAAGACTAACAGATAACCCG
Found at i:1394575 original size:21 final size:21
Alignment explanation
Indices: 1394539--1394602 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
1394529 CTTGAAAGAC
* *
1394539 TAACAGATAACCCGAAGGATT
1 TAACATATGACCCGAAGGATT
* * *
1394560 TAACATCATG-CTCGAAAGACT
1 TAACAT-ATGACCCGAAGGATT
1394581 T-ACATATGACCCGAAGGATT
1 TAACATATGACCCGAAGGATT
1394601 TA
1 TA
1394603 CAAATTCGTG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 3 0.09
20 13 0.41
21 14 0.44
22 2 0.06
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.23
Consensus pattern (21 bp):
TAACATATGACCCGAAGGATT
Found at i:1394603 original size:20 final size:21
Alignment explanation
Indices: 1394548--1394604 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
1394538 CTAACAGATA
1394548 ACCCGAAGGATTTAACATCATG
1 ACCCGAAGGATTT-ACATCATG
* * *
1394570 -CTCGAAAGACTTACAT-ATG
1 ACCCGAAGGATTTACATCATG
1394589 ACCCGAAGGATTTACA
1 ACCCGAAGGATTTACA
1394605 AATTCGTGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 3 0.11
20 16 0.57
21 9 0.32
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (21 bp):
ACCCGAAGGATTTACATCATG
Found at i:1394894 original size:247 final size:248
Alignment explanation
Indices: 1394227--1394910 Score: 1093
Period size: 248 Copynumber: 2.8 Consensus size: 248
1394217 AATTAAAGAG
* * * * *
1394227 TGTAAACATCCTGCCCAAAGGTCTGACGGATGGCCCTAAGGACTTATCATTTGGCTCGAAAGATT
1 TGTAAACATCCTACCCAAAGGTTTTACGGATGGCCCTAAGGACTTATCATCTGGCTCGAAAGACT
* * *
1394292 GATAGATGACCCGAAGGATTTAACATCATGCCCGAAAGACTTACAGATGACTCGAAGGATTTACA
66 GACAGATGACCCGAAGGATTTAACATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTACA
* * * *
1394357 AATTCATGGTAAATAATTTTCTAAGTAAGAGATTTCTTACTTTTCAAAAATTTGATTTTCTAGAA
131 AATTCGTGGAAAATAATTTACTGAGTAAGAGATTTCTTACTTTTCAAAAATTTGATTTTCTAGAA
*
1394422 CATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATA
196 CATTAAATGAGAAACTTTGAAAATCACTATCTCATTTTCATGCGAAAATCATA
* * * * *
1394475 TGTAAACATCATACCCAAAAGTTTTACGGATGGCCTTAAGGACTTATCATCTAGCTTGAAAGACT
1 TGTAAACATCCTACCCAAAGGTTTTACGGATGGCCCTAAGGACTTATCATCTGGCTCGAAAGACT
* * *
1394540 AACAGATAACCCGAAGGATTTAACATCATGCTCGAAAGACTTACATATGACCCGAAGGATTTACA
66 GACAGATGACCCGAAGGATTTAACATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTACA
* *
1394605 AATTCGT-GATAAATAATTTACTGTGTAAGAGATTTTTTACTTTTCAAAAATTTGATTTTCTAGA
131 AATTCGTGGA-AAATAATTTACTGAGTAAGAGATTTCTTACTTTTCAAAAATTTGATTTTCTAGA
1394669 ACATTAAATGAGAAACTTTGAAAATCACTATCTCATTTTCATGCGAAAATCATA
195 ACATTAAATGAGAAACTTTGAAAATCACTATCTCATTTTCATGCGAAAATCATA
1394723 TGTAAACATCCTACCCAAAGGTTTTAC-GATGGCCCTAAGGACTTATCATCTGGCTCGAAAGACT
1 TGTAAACATCCTACCCAAAGGTTTTACGGATGGCCCTAAGGACTTATCATCTGGCTCGAAAGACT
* * *
1394787 GACAGATGACTCGAAGGATTTAAAATCATGCTTGAAAGACTTACAGATGACCCGAAGGATTTACA
66 GACAGATGACCCGAAGGATTTAACATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTACA
* *
1394852 AATTCGTGGAAAATAATTTACTGAGTAAGAGATTTCTTACTTTTCAATAATTTCATTTT
131 AATTCGTGGAAAATAATTTACTGAGTAAGAGATTTCTTACTTTTCAAAAATTTGATTTT
1394911 TTTTGGAAAA
Statistics
Matches: 396, Mismatches: 38, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
247 146 0.37
248 250 0.63
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (248 bp):
TGTAAACATCCTACCCAAAGGTTTTACGGATGGCCCTAAGGACTTATCATCTGGCTCGAAAGACT
GACAGATGACCCGAAGGATTTAACATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTACA
AATTCGTGGAAAATAATTTACTGAGTAAGAGATTTCTTACTTTTCAAAAATTTGATTTTCTAGAA
CATTAAATGAGAAACTTTGAAAATCACTATCTCATTTTCATGCGAAAATCATA
Found at i:1395708 original size:65 final size:65
Alignment explanation
Indices: 1395626--1395750 Score: 180
Period size: 65 Copynumber: 1.9 Consensus size: 65
1395616 TCTGATTTGA
* * * *
1395626 CTCTTGAAACACATCATAAGAAGGATTTATCTTAATTCTTTTCATGTCTCCACATATAATCATAT
1 CTCTTGAAACACATCATAAAAAGGATTCATCCTAATTCCTTTCATGTCTCCACATATAATCATAT
* *
1395691 CTCTTGAAATAGC-TCATAAAAAGGATTCATCCTAATTCCTTTCATGTCTCCACATCTAAT
1 CTCTTGAAACA-CATCATAAAAAGGATTCATCCTAATTCCTTTCATGTCTCCACATATAAT
1395751 TAGATCTCGA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 52 0.98
66 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (65 bp):
CTCTTGAAACACATCATAAAAAGGATTCATCCTAATTCCTTTCATGTCTCCACATATAATCATAT
Found at i:1403352 original size:22 final size:18
Alignment explanation
Indices: 1403315--1403374 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 18
1403305 TGTAAATGCA
1403315 AATATAATAAAATAATAT
1 AATATAATAAAATAATAT
*
1403333 ATATATAAT-AAAT-ATGT
1 A-ATATAATAAAATAATAT
1403350 AATATAAT--AATAATAT
1 AATATAATAAAATAATAT
1403366 AAT-TAATAA
1 AATATAATAA
1403375 TAAAAATAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 7 0.19
16 13 0.36
17 4 0.11
18 5 0.14
19 7 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AATATAATAAAATAATAT
Found at i:1403354 original size:18 final size:17
Alignment explanation
Indices: 1403316--1403382 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 17
1403306 GTAAATGCAA
*
1403316 ATATAATAAAATAATATAT
1 ATATAAT-AAATATTA-AT
1403335 ATATAATAAATATGTAAT
1 ATATAATAAATAT-TAAT
1403353 ATAATAATAATATAATTAAT
1 AT-ATAATAA-AT-ATTAAT
1403373 A-ATAA-AAATA
1 ATATAATAAATA
1403383 GACAAAAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
15 1 0.02
16 2 0.05
17 2 0.05
18 13 0.30
19 16 0.37
20 7 0.16
21 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (17 bp):
ATATAATAAATATTAAT
Found at i:1403367 original size:11 final size:11
Alignment explanation
Indices: 1403315--1403376 Score: 56
Period size: 11 Copynumber: 5.4 Consensus size: 11
1403305 TGTAAATGCA
1403315 AATATAATAA-
1 AATATAATAAT
1403325 AATAATATATATAT
1 AAT-ATA-ATA-AT
*
1403339 AATA-AATATGT
1 AATATAATA-AT
1403350 AATATAATAAT
1 AATATAATAAT
1403361 AATATAATTAAT
1 AATATAA-TAAT
1403373 AATA
1 AATA
1403377 AAAATAGACA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
10 3 0.07
11 20 0.45
12 16 0.36
13 2 0.05
14 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
AATATAATAAT
Found at i:1403372 original size:15 final size:16
Alignment explanation
Indices: 1403315--1403377 Score: 71
Period size: 15 Copynumber: 4.1 Consensus size: 16
1403305 TGTAAATGCA
*
1403315 AATATAATAAAATAAT
1 AATATAATATAATAAT
1403331 -ATAT-ATATAATAA-
1 AATATAATATAATAAT
*
1403344 ATATGTAATATAATAAT
1 A-ATATAATATAATAAT
1403361 AATATAAT-TAATAAT
1 AATATAATATAATAAT
1403376 AA
1 AA
1403378 AAATAGACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
14 8 0.20
15 16 0.40
16 15 0.38
17 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
AATATAATATAATAAT
Found at i:1407632 original size:14 final size:14
Alignment explanation
Indices: 1407613--1407683 Score: 70
Period size: 14 Copynumber: 4.7 Consensus size: 14
1407603 CATGAGTTAG
1407613 TAAACTAATCATAA
1 TAAACTAATCATAA
*
1407627 TAAACTAATCATTTA
1 TAAACTAATCA-TAA
**
1407642 TATCCTTTATTATCATAA
1 TAAAC--TA--ATCATAA
1407660 TAAACTAATCATAA
1 TAAACTAATCATAA
1407674 TAAACTAATC
1 TAAACTAATC
1407684 GTTTATATCC
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 28 0.61
15 5 0.11
16 2 0.04
17 2 0.04
18 5 0.11
19 4 0.09
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAACTAATCATAA
Found at i:1407666 original size:47 final size:47
Alignment explanation
Indices: 1407613--1407720 Score: 198
Period size: 47 Copynumber: 2.3 Consensus size: 47
1407603 CATGAGTTAG
*
1407613 TAAACTAATCATAATAAACTAATCATTTATATCCTTTATTATCATAA
1 TAAACTAATCATAATAAACTAATCATTTATATCCTTTACTATCATAA
*
1407660 TAAACTAATCATAATAAACTAATCGTTTATATCCTTTACTATCATAA
1 TAAACTAATCATAATAAACTAATCATTTATATCCTTTACTATCATAA
1407707 TAAACTAATCATAA
1 TAAACTAATCATAA
1407721 CCAAAGGAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.45, C:0.16, G:0.01, T:0.38
Consensus pattern (47 bp):
TAAACTAATCATAATAAACTAATCATTTATATCCTTTACTATCATAA
Found at i:1410801 original size:13 final size:13
Alignment explanation
Indices: 1410783--1410815 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1410773 AATTCTGTTC
1410783 AGAATAATAAAAA
1 AGAATAATAAAAA
1410796 AGAATAAATAAAAA
1 AGAAT-AATAAAAA
1410810 A-AATAA
1 AGAATAA
1410816 AACAGAGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 8 0.42
14 9 0.47
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (13 bp):
AGAATAATAAAAA
Found at i:1410816 original size:13 final size:14
Alignment explanation
Indices: 1410783--1410816 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1410773 AATTCTGTTC
1410783 AGAAT-AATAAAAA
1 AGAATAAATAAAAA
1410796 AGAATAAATAAAAA
1 AGAATAAATAAAAA
1410810 A-AATAAA
1 AGAATAAA
1410817 ACAGAGACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (14 bp):
AGAATAAATAAAAA
Found at i:1412890 original size:23 final size:23
Alignment explanation
Indices: 1412856--1412902 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1412846 TAATAAATTT
*
1412856 ATAAATTTTTAAAAA-GATAAAAA
1 ATAAATTATTAAAAATGA-AAAAA
1412879 ATAAATTATTAAAAATGAAAAAA
1 ATAAATTATTAAAAATGAAAAAA
1412902 A
1 A
1412903 GTATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (23 bp):
ATAAATTATTAAAAATGAAAAAA
Found at i:1414485 original size:2 final size:2
Alignment explanation
Indices: 1414478--1414507 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1414468 GATAGTTTTA
1414478 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
1414508 TAACCTTAAA
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:1417927 original size:3 final size:3
Alignment explanation
Indices: 1417919--1417945 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1417909 GAATAGGGTT
1417919 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1417946 CTCTATGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:1424522 original size:31 final size:31
Alignment explanation
Indices: 1424496--1424608 Score: 104
Period size: 31 Copynumber: 3.6 Consensus size: 31
1424486 TCCATAGGTC
*
1424496 CCGAAGAACCTAGGTAAACTGTCCATATGAT
1 CCGAAGAACATAGGTAAACTGTCCATATGAT
** *
1424527 CCTTAGAACATAGGTATACTGTCCATATG-T
1 CCGAAGAACATAGGTAAACTGTCCATATGAT
* ** *
1424557 CTC-AAAATACATAGGTAATTTTGTCCATATGTT
1 C-CGAAGA-ACATAGGTAA-ACTGTCCATATGAT
*
1424590 CCGTAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
1424609 CCTCGACTCT
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
30 4 0.06
31 35 0.55
32 21 0.33
33 4 0.06
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACTGTCCATATGAT
Found at i:1430753 original size:16 final size:16
Alignment explanation
Indices: 1430732--1430794 Score: 99
Period size: 16 Copynumber: 3.9 Consensus size: 16
1430722 TTACCCGACC
1430732 TGTTTTTAACCTGACA
1 TGTTTTTAACCTGACA
*
1430748 TGTTTTTAACCTGACC
1 TGTTTTTAACCTGACA
*
1430764 TGTTTTTAACCTGACT
1 TGTTTTTAACCTGACA
*
1430780 TGTTTTTAACTTGAC
1 TGTTTTTAACCTGAC
1430795 CTGTAAATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.48
Consensus pattern (16 bp):
TGTTTTTAACCTGACA
Found at i:1430769 original size:32 final size:32
Alignment explanation
Indices: 1430728--1430798 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1430718 GGTATTACCC
1430728 GACCTGTTTTTAACCTGACATGTTTTTAACCT
1 GACCTGTTTTTAACCTGACATGTTTTTAACCT
* *
1430760 GACCTGTTTTTAACCTGACTTGTTTTTAACTT
1 GACCTGTTTTTAACCTGACATGTTTTTAACCT
1430792 GACCTGT
1 GACCTGT
1430799 AAATGATCCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (32 bp):
GACCTGTTTTTAACCTGACATGTTTTTAACCT
Found at i:1431008 original size:13 final size:13
Alignment explanation
Indices: 1430992--1431018 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1430982 TACCTATTAT
1430992 ATAAAATTATTTA
1 ATAAAATTATTTA
1431005 ATAAAATTATTTA
1 ATAAAATTATTTA
1431018 A
1 A
1431019 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:1431091 original size:23 final size:24
Alignment explanation
Indices: 1431057--1431106 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
1431047 ATGCAAAAAA
*
1431057 AAATTAATATAGTTTGATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1431081 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1431104 AAA
1 AAA
1431107 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:1431395 original size:11 final size:11
Alignment explanation
Indices: 1431355--1431393 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1431345 TGATAATGAT
1431355 AATTTAAATAA
1 AATTTAAATAA
*
1431366 CATTTAATATAA
1 AATTTAA-ATAA
*
1431378 AATTTGAATAA
1 AATTTAAATAA
1431389 AATTT
1 AATTT
1431394 GAGTTAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (11 bp):
AATTTAAATAA
Found at i:1433308 original size:22 final size:22
Alignment explanation
Indices: 1433280--1433343 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
1433270 GGTACACACA
1433280 CATACATGTATACAAATTATAT
1 CATACATGTATACAAATTATAT
*
1433302 CATACATAG-GTACAAA--A-A-
1 CATACAT-GTATACAAATTATAT
1433320 CATACATGTATACAAATTATAT
1 CATACATGTATACAAATTATAT
1433342 CA
1 CA
1433344 AATTCATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
17 1 0.03
18 13 0.38
19 1 0.03
20 2 0.06
21 1 0.03
22 15 0.44
23 1 0.03
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30
Consensus pattern (22 bp):
CATACATGTATACAAATTATAT
Found at i:1433310 original size:40 final size:40
Alignment explanation
Indices: 1433248--1433343 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
1433238 ATCTCCATTA
* * * * *
1433248 TATATAAATTATATTATGCATAGGTACACACACATACATG
1 TATACAAATTATATCATACATAGGTACAAAAACATACATG
1433288 TATACAAATTATATCATACATAGGTACAAAAACATACATG
1 TATACAAATTATATCATACATAGGTACAAAAACATACATG
1433328 TATACAAATTATATCA
1 TATACAAATTATATCA
1433344 AATTCATACA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (40 bp):
TATACAAATTATATCATACATAGGTACAAAAACATACATG
Found at i:1433333 original size:18 final size:20
Alignment explanation
Indices: 1433279--1433336 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 20
1433269 AGGTACACAC
1433279 ACATACATGTATACAAATTAT
1 ACATACATGTATACAAA-TAT
*
1433300 ATCATACATAG-GTACAAA-A-
1 A-CATACAT-GTATACAAATAT
1433319 ACATACATGTATACAAAT
1 ACATACATGTATACAAAT
1433337 TATATCAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
17 1 0.03
18 13 0.42
19 1 0.03
20 1 0.03
21 1 0.03
22 13 0.42
23 1 0.03
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.28
Consensus pattern (20 bp):
ACATACATGTATACAAATAT
Found at i:1433726 original size:15 final size:14
Alignment explanation
Indices: 1433699--1433733 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1433689 AAAGAATACA
1433699 AATTGGAAAAAAATG
1 AATT-GAAAAAAATG
1433714 AATTGAAAGAAAATG
1 AATTGAAA-AAAATG
1433729 AATTG
1 AATTG
1433734 GCAGCAGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (14 bp):
AATTGAAAAAAATG
Found at i:1434219 original size:6 final size:6
Alignment explanation
Indices: 1434181--1434331 Score: 57
Period size: 6 Copynumber: 24.3 Consensus size: 6
1434171 ATTTTTATTA
*
1434181 ATTAACT ATTTAT AATTAAT ATTATAAT AATTAAT ATT-AT AATT-AT
1 ATTAA-T ATTAAT -ATTAAT A-T-TAAT -ATTAAT ATTAAT -ATTAAT
*
1434227 AATTAAT A-T-A- ATTAAT ATTAAT ATTAA- ATT-AT ATTAAT ATAATAT
1 -ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTA-AT
* * * * * *
1434272 AGTTTAT AATTTAT AATTAAT ATTAAT A-TAAA ATATAGT CTATAAC ATTAAT
1 A-TTAAT -ATTAAT -ATTAAT ATTAAT ATTAAT AT-TAAT AT-TAAT ATTAAT
1434324 ATTAAT AT
1 ATTAAT AT
1434332 AAATTATATG
Statistics
Matches: 114, Mismatches: 14, Indels: 33
0.71 0.09 0.20
Matches are distributed among these distances:
3 1 0.01
4 3 0.03
5 14 0.12
6 49 0.43
7 39 0.34
8 7 0.06
9 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (6 bp):
ATTAAT
Found at i:1434220 original size:27 final size:27
Alignment explanation
Indices: 1434179--1434271 Score: 95
Period size: 27 Copynumber: 3.4 Consensus size: 27
1434169 TAATTTTTAT
1434179 TAATTAACTATTTATAATTAATATTATAA
1 TAATTAA-TA-TTATAATTAATATTATAA
1434208 TAATTAATATTATAATT-ATAATTA-ATA
1 TAATTAATATTATAATTAAT-ATTATA-A
*
1434235 TAATTAATATTA-ATATTAA-ATTATAT
1 TAATTAATATTATA-ATTAATATTATAA
1434261 TAATATAATAT
1 TAAT-TAATAT
1434272 AGTTTATAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
26 12 0.21
27 35 0.61
28 3 0.05
29 7 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (27 bp):
TAATTAATATTATAATTAATATTATAA
Found at i:1434225 original size:21 final size:20
Alignment explanation
Indices: 1434201--1434296 Score: 66
Period size: 18 Copynumber: 4.9 Consensus size: 20
1434191 TATAATTAAT
1434201 ATTATAATAATTAATATTATA
1 ATTAT-ATAATTAATATTATA
1434222 A-T-TATAATT-A-A-TATA
1 ATTATATAATTAATATTATA
1434237 ATTA-AT-ATTAATATTA-A
1 ATTATATAATTAATATTATA
1434254 ATTATATTAATATAATATAGTTTATA
1 ATTATA-TAAT-T-A-ATA--TTATA
1434280 ATT-TATAATTAATATTA
1 ATTATATAATTAATATTA
1434297 ATATAAAATA
Statistics
Matches: 61, Mismatches: 0, Indels: 30
0.67 0.00 0.33
Matches are distributed among these distances:
15 8 0.13
16 5 0.08
17 7 0.11
18 9 0.15
19 5 0.08
20 3 0.05
21 5 0.08
22 2 0.03
23 4 0.07
24 4 0.07
25 5 0.08
26 4 0.07
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
ATTATATAATTAATATTATA
Found at i:1434285 original size:27 final size:26
Alignment explanation
Indices: 1434167--1434301 Score: 91
Period size: 27 Copynumber: 4.9 Consensus size: 26
1434157 TTCATCTTTA
* *
1434167 TATAATTTTTATTAAT-TAA-CTATT
1 TATAATTTATATTAATATAATATATT
*
1434191 TATAATTAATATT-ATAATAAT-TAATAT
1 TATAATTTATATTAAT-ATAATAT-AT-T
1434218 TATAA-TTATAATTAATATAATTAATATT
1 TATAATTTAT-ATTAATATAA-T-ATATT
*
1434246 AATATTAAATTATATTAATATAATATAGTT
1 --TA-TAATTTATATTAATATAATATA-TT
1434276 TATAATTTATAATTAATATTAATATA
1 TATAATTTAT-ATTAATA-TAATATA
1434302 AAATATAGTC
Statistics
Matches: 90, Mismatches: 4, Indels: 29
0.73 0.03 0.24
Matches are distributed among these distances:
23 2 0.02
24 11 0.12
25 4 0.04
26 5 0.06
27 20 0.22
28 13 0.14
29 12 0.13
30 6 0.07
31 13 0.14
32 4 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (26 bp):
TATAATTTATATTAATATAATATATT
Found at i:1434307 original size:36 final size:33
Alignment explanation
Indices: 1434212--1434327 Score: 112
Period size: 33 Copynumber: 3.4 Consensus size: 33
1434202 TTATAATAAT
* *
1434212 TAATATTATAATTATAATTAATATAAT-TAATAT-
1 TAATATTA-AATTAT-ATTAATATAATATAGTCTA
*
1434245 TAATATTAAATTATATTAATATAATATAGTTTA
1 TAATATTAAATTATATTAATATAATATAGTCTA
1434278 TAAT-TTATAATTAATATTAATATAAAATATAGTCTA
1 TAATATTA-AATT-ATATTAATAT--AATATAGTCTA
*
1434314 TAACATTAATATTA
1 TAATATTAA-ATTA
1434328 ATATAAATTA
Statistics
Matches: 71, Mismatches: 4, Indels: 13
0.81 0.05 0.15
Matches are distributed among these distances:
31 11 0.15
32 13 0.18
33 16 0.23
34 10 0.14
36 15 0.21
37 6 0.08
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (33 bp):
TAATATTAAATTATATTAATATAATATAGTCTA
Found at i:1434325 original size:31 final size:30
Alignment explanation
Indices: 1434282--1434351 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 30
1434272 AGTTTATAAT
1434282 TTAT-AATTAATATTAATATAAAATATA-G
1 TTATAAATTAATATTAATATAAAATATATG
*
1434310 TCTATAACATTAATATTAATATAAATTATATG
1 T-TATAA-ATTAATATTAATATAAAATATATG
1434342 TTATAAATTA
1 TTATAAATTA
1434352 TATAGTATAG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 1 0.03
29 3 0.08
30 5 0.14
31 26 0.70
32 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (30 bp):
TTATAAATTAATATTAATATAAAATATATG
Found at i:1434410 original size:20 final size:21
Alignment explanation
Indices: 1434369--1434410 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1434359 TAGTTTATTA
1434369 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
1434391 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
1434411 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:1434532 original size:24 final size:24
Alignment explanation
Indices: 1434503--1434560 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1434493 ATATATAATT
*
1434503 TATATA-ACATATA-AATAGATTG
1 TATATATACATATACAATAGATTA
* *
1434525 TATATATACATATACTATAGGTTA
1 TATATATACATATACAATAGATTA
1434549 TATATATACATA
1 TATATATACATA
1434561 GTTTATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 6 0.19
23 7 0.23
24 18 0.58
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (24 bp):
TATATATACATATACAATAGATTA
Found at i:1434552 original size:20 final size:19
Alignment explanation
Indices: 1434527--1434591 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
1434517 ATAGATTGTA
1434527 TATATACATATACTATAGGT
1 TATATACATATAC-ATAGGT
*
1434547 TATAT--ATATACATAGTT
1 TATATACATATACATAGGT
1434564 TATATACACTATACATA-GT
1 TATATACA-TATACATAGGT
1434583 T-TATACATA
1 TATATACATA
1434592 CATGATACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 12 0.30
18 12 0.30
19 3 0.08
20 13 0.32
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (19 bp):
TATATACATATACATAGGT
Found at i:1434638 original size:37 final size:37
Alignment explanation
Indices: 1434590--1434660 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
1434580 AGTTTATACA
*
1434590 TACATGATACATGTA-CTATAAGTTACATT-TATAGTT
1 TACATGATACATATATC-ATAAGTTACATTATATAGTT
*
1434626 TACATGTATACATATATCATAGGTTACATTATATA
1 TACATG-ATACATATATCATAAGTTACATTATATA
1434661 TATTAACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 6 0.20
37 19 0.63
38 5 0.17
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (37 bp):
TACATGATACATATATCATAAGTTACATTATATAGTT
Found at i:1434732 original size:7 final size:7
Alignment explanation
Indices: 1434722--1434798 Score: 72
Period size: 7 Copynumber: 11.4 Consensus size: 7
1434712 AGATTTAAAA
*
1434722 TTTAGAG
1 TTTAGGG
1434729 TTTAGGG
1 TTTAGGG
1434736 TTTAGGG
1 TTTAGGG
*
1434743 TTT-TGG
1 TTTAGGG
1434749 TTTAGGG
1 TTTAGGG
*
1434756 TTTAAGGT
1 TTT-AGGG
1434764 TTTA--G
1 TTTAGGG
*
1434769 TTTAGGA
1 TTTAGGG
*
1434776 TTT-TGG
1 TTTAGGG
1434782 TTTAGGG
1 TTTAGGG
1434789 TTTAGGG
1 TTTAGGG
1434796 TTT
1 TTT
1434799 TATATAATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
5 4 0.07
6 9 0.16
7 37 0.66
8 6 0.11
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.51
Consensus pattern (7 bp):
TTTAGGG
Found at i:1434752 original size:13 final size:13
Alignment explanation
Indices: 1434734--1434758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1434724 TAGAGTTTAG
1434734 GGTTTAGGGTTTT
1 GGTTTAGGGTTTT
1434747 GGTTTAGGGTTT
1 GGTTTAGGGTTT
1434759 AAGGTTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.40, T:0.52
Consensus pattern (13 bp):
GGTTTAGGGTTTT
Found at i:1434780 original size:33 final size:33
Alignment explanation
Indices: 1434735--1434800 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1434725 AGAGTTTAGG
*
1434735 GTTTAGGGTTTTGGTTTAGGGTTTAAGGTTTTA
1 GTTTAGGATTTTGGTTTAGGGTTTAAGGTTTTA
*
1434768 GTTTAGGATTTTGGTTTAGGGTTTAGGGTTTTA
1 GTTTAGGATTTTGGTTTAGGGTTTAAGGTTTTA
1434801 TATAATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (33 bp):
GTTTAGGATTTTGGTTTAGGGTTTAAGGTTTTA
Found at i:1434799 original size:20 final size:20
Alignment explanation
Indices: 1434728--1434798 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1434718 AAAATTTAGA
*
1434728 GTTTAGGGTTTAGGGTTTTG
1 GTTTAGGGTTTAAGGTTTTG
*
1434748 GTTTAGGGTTTAAGGTTTTA
1 GTTTAGGGTTTAAGGTTTTG
* * *
1434768 GTTTAGGATTT-TGGTTTAGG
1 GTTTAGGGTTTAAGGTTT-TG
1434788 GTTTAGGGTTT
1 GTTTAGGGTTT
1434799 TATATAATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 5 0.12
20 38 0.88
ACGTcount: A:0.14, C:0.00, G:0.35, T:0.51
Consensus pattern (20 bp):
GTTTAGGGTTTAAGGTTTTG
Found at i:1435265 original size:76 final size:76
Alignment explanation
Indices: 1435183--1435331 Score: 219
Period size: 76 Copynumber: 2.0 Consensus size: 76
1435173 TTATACATAC
*
1435183 ATATATATACTATATAAATATAAATTATAACAGATAAACTATATA-TTTTATATAATTTATACAT
1 ATATATATACTATATAAATATAAATAATAACAGATAAACTATATACTTTT-TATAATTTATACAT
1435247 ATATAGTTTTTT
65 ATATAGTTTTTT
* **** *
1435259 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATACATA
1 ATATATATACTATATAAATATAAATAATAACAGATAAACTATATACTTTTTATAATTTATACATA
1435324 TATAGTTT
66 TATAGTTT
1435332 ATATACATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
76 61 0.94
77 4 0.06
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (76 bp):
ATATATATACTATATAAATATAAATAATAACAGATAAACTATATACTTTTTATAATTTATACATA
TATAGTTTTTT
Found at i:1435267 original size:24 final size:23
Alignment explanation
Indices: 1435220--1435273 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1435210 TAACAGATAA
*
1435220 ACTATATATTTTATATAATTTAT
1 ACTATATATTTTATATAATATAT
*
1435243 ACATATATAGTTTTTTAT-ATATAT
1 AC-TATATA-TTTTATATAATATAT
1435267 ACTATAT
1 ACTATAT
1435274 TAATATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.26
24 13 0.48
25 7 0.26
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (23 bp):
ACTATATATTTTATATAATATAT
Found at i:1435359 original size:13 final size:13
Alignment explanation
Indices: 1435309--1435505 Score: 101
Period size: 13 Copynumber: 15.3 Consensus size: 13
1435299 ATATACTTTT
1435309 TATAGTTTATACATA
1 TATAGTTTAT--ATA
1435324 TATAGTTTATATA
1 TATAGTTTATATA
* *
1435337 CATAATTTATATA
1 TATAGTTTATATA
*
1435350 TATAGCTTATA-A
1 TATAGTTTATATA
1435362 TA-A--TTATATA
1 TATAGTTTATATA
* * *
1435372 GTTTA-TAATATAAA
1 -TATAGT-TTATATA
1435386 TATAGTTTATATA
1 TATAGTTTATATA
*
1435399 CATAGTTTATATA
1 TATAGTTTATATA
** *
1435412 TATAGTGCACATAAA
1 TATAGT--TTATATA
*
1435427 TATAATTTATATA
1 TATAGTTTATATA
1435440 TATAGTTTATA-A
1 TATAGTTTATATA
1435452 TA-A--TTATATA
1 TATAGTTTATATA
* * *
1435462 GTTTA-TAATATAAA
1 -TATAGT-TTATATA
1435476 TATAGTTTATATA
1 TATAGTTTATATA
*
1435489 TA-ATTTTATATTA
1 TATAGTTTATA-TA
1435502 TATA
1 TATA
1435506 TATTATATTT
Statistics
Matches: 138, Mismatches: 28, Indels: 33
0.69 0.14 0.17
Matches are distributed among these distances:
9 10 0.07
10 2 0.01
11 4 0.03
12 15 0.11
13 75 0.54
14 13 0.09
15 19 0.14
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:1435361 original size:20 final size:19
Alignment explanation
Indices: 1435338--1435380 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1435328 GTTTATATAC
*
1435338 ATAATTTATATATATAGCTT
1 ATAATTAAT-TATATAGCTT
*
1435358 ATAA-TAATTATATAGTTT
1 ATAATTAATTATATAGCTT
1435376 ATAAT
1 ATAAT
1435381 ATAAATATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 13 0.65
19 3 0.15
20 4 0.20
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (19 bp):
ATAATTAATTATATAGCTT
Found at i:1435388 original size:18 final size:18
Alignment explanation
Indices: 1435344--1435491 Score: 71
Period size: 18 Copynumber: 8.3 Consensus size: 18
1435334 ATACATAATT
* *
1435344 TATATATATAGCTTATAA
1 TATAAATATAGTTTATAA
*
1435362 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
1435380 TATAAATATAGTTTATATACA
1 TATAAATATAG-TT-TATA-A
** * *
1435401 TAGTTTATATA-TATAGTGCA
1 TA-TAAATATAGTTTA-T-AA
* *
1435421 CATAAATATAATTTAT-A
1 TATAAATATAGTTTATAA
1435438 TAT----ATAGTTTATAA
1 TATAAATATAGTTTATAA
*
1435452 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
1435470 TATAAATATAGTTTAT-A
1 TATAAATATAGTTTATAA
1435487 TATAA
1 TATAA
1435492 TTTTATATTA
Statistics
Matches: 101, Mismatches: 13, Indels: 33
0.69 0.09 0.22
Matches are distributed among these distances:
13 8 0.08
14 3 0.03
17 10 0.10
18 47 0.47
19 13 0.13
20 11 0.11
21 3 0.03
22 6 0.06
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TATAAATATAGTTTATAA
Found at i:1435435 original size:90 final size:90
Alignment explanation
Indices: 1435338--1435505 Score: 293
Period size: 90 Copynumber: 1.9 Consensus size: 90
1435328 GTTTATATAC
1435338 ATAATTTATATATATAGCTTATAATAATTATATAGTTTATAATATAAATATAGTTTATATACATA
1 ATAATTTATATATATAGCTTATAATAATTATATAGTTTATAATATAAATATAGTTTATATACA-A
1435403 GTTTATA-TATATAGTGCACATAAAT
65 GTTTATATTATATAGTGCACATAAAT
* * *
1435428 ATAATTTATATATATAGTTTATAATAATTATATAGTTTATAATATAAATATAGTTTATATATAAT
1 ATAATTTATATATATAGCTTATAATAATTATATAGTTTATAATATAAATATAGTTTATATACAAG
1435493 TTTATATTATATA
66 TTTATATTATATA
1435506 TATTATATTT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
89 7 0.09
90 67 0.91
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (90 bp):
ATAATTTATATATATAGCTTATAATAATTATATAGTTTATAATATAAATATAGTTTATATACAAG
TTTATATTATATAGTGCACATAAAT
Found at i:1435451 original size:26 final size:26
Alignment explanation
Indices: 1435380--1435451 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 26
1435370 TAGTTTATAA
* * *
1435380 TATAAATATAGTTTATATACATAGTT
1 TATATATATAGTTTATAAACATAATT
** *
1435406 TATATATATAGTGCACATAAATATAATT
1 TATATATATAGT--TTATAAACATAATT
1435434 TATATATATAGTTTATAA
1 TATATATATAGTTTATAA
1435452 TAATTATATA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 15 0.42
28 21 0.58
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (26 bp):
TATATATATAGTTTATAAACATAATT
Found at i:1441235 original size:20 final size:21
Alignment explanation
Indices: 1441187--1441236 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
1441177 GATATATTTT
* * *
1441187 AATTATTAATTTATTCAATAA
1 AATTATAAATCTATCCAATAA
1441208 ATATTATAAATCTATCCAA-AA
1 A-ATTATAAATCTATCCAATAA
1441229 AATTATAA
1 AATTATAA
1441237 CATAACAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 7 0.28
21 4 0.16
22 14 0.56
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTATAAATCTATCCAATAA
Found at i:1448096 original size:14 final size:14
Alignment explanation
Indices: 1448050--1448101 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 14
1448040 AAGTGTGAGG
*
1448050 ATAATTAGAAAAAT
1 ATAATTATAAAAAT
*
1448064 AATATTTATAAAATGAT
1 -ATAATTATAAAA--AT
1448081 ATAATTATAAAAAT
1 ATAATTATAAAAAT
*
1448095 ATTATTA
1 ATAATTA
1448102 AATAAGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 8 0.26
15 10 0.32
16 11 0.35
17 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (14 bp):
ATAATTATAAAAAT
Found at i:1449021 original size:24 final size:23
Alignment explanation
Indices: 1448994--1449047 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
1448984 TCAAACAACT
1448994 ACGAAAGAAAATGAAAAACGTGTC
1 ACGAAAGAAAA-GAAAAACGTGTC
* * * *
1449018 ACGAACGCATAGAAAAATGTGTC
1 ACGAAAGAAAAGAAAAACGTGTC
1449041 AC-AAAGA
1 ACGAAAGA
1449048 CATAATTGAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 3 0.12
23 13 0.54
24 8 0.33
ACGTcount: A:0.52, C:0.15, G:0.20, T:0.13
Consensus pattern (23 bp):
ACGAAAGAAAAGAAAAACGTGTC
Found at i:1449051 original size:23 final size:23
Alignment explanation
Indices: 1449006--1449051 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1448996 GAAAGAAAAT
*
1449006 GAAAAACGTGTCACGAACGCATA
1 GAAAAACGTGTCACGAAAGCATA
*
1449029 GAAAAATGTGTCAC-AAAGACATA
1 GAAAAACGTGTCACGAAAG-CATA
1449052 ATTGATCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (23 bp):
GAAAAACGTGTCACGAAAGCATA
Found at i:1458313 original size:21 final size:21
Alignment explanation
Indices: 1458289--1458328 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1458279 TATTTAATAT
1458289 GAAAATTCAGATATTTGATCC
1 GAAAATTCAGATATTTGATCC
**
1458310 GAAAATTTGGATATTTGAT
1 GAAAATTCAGATATTTGAT
1458329 TTTTTGGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (21 bp):
GAAAATTCAGATATTTGATCC
Found at i:1458497 original size:21 final size:20
Alignment explanation
Indices: 1458465--1458516 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1458455 CCAAAAGTTT
* *
1458465 TTCTATTAAAAATTATTAAC
1 TTCTTTTAAAAATAATTAAC
*
1458485 TTCTTTTAGAAAATAATTAAT
1 TTCTTTTA-AAAATAATTAAC
*
1458506 TTATTTTAAAA
1 TTCTTTTAAAA
1458517 CACTGTTACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (20 bp):
TTCTTTTAAAAATAATTAAC
Found at i:1458873 original size:51 final size:51
Alignment explanation
Indices: 1458809--1458939 Score: 172
Period size: 51 Copynumber: 2.6 Consensus size: 51
1458799 AATTCATATT
* * *
1458809 ATAAAAAAATGTAGCACTTAACTCATATTTACATCGGTGTAAGTGAATAAA
1 ATAAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAA
* * *
1458860 ATAAACAAGTGTAGCACTTAACACATACTTACACCGGTGTGAGTGAATAAA
1 ATAAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAA
* * * *
1458911 ATAAAAAAATATAACATTTAATACATACT
1 ATAAAAAAATGTAGCACTTAACACATACT
1458940 CTAAAATAGT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (51 bp):
ATAAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAA
Found at i:1459153 original size:20 final size:20
Alignment explanation
Indices: 1459130--1459173 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1459120 CTGTATAAAT
1459130 AGTACTAATACTGTTTGAAC
1 AGTACTAATACTGTTTGAAC
* *
1459150 AGTACTGATATTGTTTGAAC
1 AGTACTAATACTGTTTGAAC
1459170 AGTA
1 AGTA
1459174 ATTAACAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (20 bp):
AGTACTAATACTGTTTGAAC
Found at i:1462078 original size:17 final size:16
Alignment explanation
Indices: 1462046--1462100 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
1462036 GTTTGTTATT
1462046 TTTTGTTGAAA-TTCAA
1 TTTTGTT-AAAGTTCAA
1462062 TTTTGTTAAAGTGTCAA
1 TTTTGTTAAAGT-TCAA
* * *
1462079 GTTT-TTAAAGCTAAA
1 TTTTGTTAAAGTTCAA
1462094 TTTTGTT
1 TTTTGTT
1462101 TGGAATGCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 9 0.28
16 16 0.50
17 7 0.22
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (16 bp):
TTTTGTTAAAGTTCAA
Found at i:1462614 original size:20 final size:19
Alignment explanation
Indices: 1462586--1462635 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1462576 ATTTACTATA
*
1462586 TAAATAGTATTGATACTGTT
1 TAAACAGTATT-ATACTGTT
* *
1462606 TGAACAGTACTTATATTGTT
1 TAAACAGTA-TTATACTGTT
1462626 TAAACAGTAT
1 TAAACAGTAT
1462636 CCGAGGCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 22 0.88
21 2 0.08
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (19 bp):
TAAACAGTATTATACTGTT
Found at i:1462749 original size:20 final size:20
Alignment explanation
Indices: 1462721--1462758 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1462711 TTAAATTTTA
*
1462721 TGAAAGGGTATCGATACCAT
1 TGAAAGGGTACCGATACCAT
*
1462741 TGAAGGGGTACCGATACC
1 TGAAAGGGTACCGATACC
1462759 CCCTGTACGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (20 bp):
TGAAAGGGTACCGATACCAT
Found at i:1464840 original size:41 final size:42
Alignment explanation
Indices: 1464779--1464887 Score: 159
Period size: 41 Copynumber: 2.6 Consensus size: 42
1464769 CATCTTATCA
*
1464779 AATAAGTCTCAATAAATCTAAAATAAATAACACCATAAC-AC
1 AATAAGTCTCAATAAGTCTAAAATAAATAACACCATAACAAC
* * * *
1464820 CATAAGTTTAAATAAGTCTAAAATAAATAACACCATAACAAT
1 AATAAGTCTCAATAAGTCTAAAATAAATAACACCATAACAAC
1464862 AATAAGTCTCAATAAGTCT-AAATAAA
1 AATAAGTCTCAATAAGTCTAAAATAAA
1464888 ATCAACATCA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
41 42 0.71
42 17 0.29
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.25
Consensus pattern (42 bp):
AATAAGTCTCAATAAGTCTAAAATAAATAACACCATAACAAC
Found at i:1481722 original size:20 final size:20
Alignment explanation
Indices: 1481688--1481727 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1481678 ATTTAAATGA
*
1481688 TAAACGAACATAAACAAACG
1 TAAACGAACACAAACAAACG
* *
1481708 TAAACGAGCACAAACGAACG
1 TAAACGAACACAAACAAACG
1481728 AACATAAACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.23, G:0.15, T:0.07
Consensus pattern (20 bp):
TAAACGAACACAAACAAACG
Found at i:1481736 original size:14 final size:13
Alignment explanation
Indices: 1481716--1481749 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1481706 CGTAAACGAG
1481716 CACAAACGAACGAA
1 CACAAACGAAC-AA
*
1481730 CATAAACGAACAA
1 CACAAACGAACAA
1481743 CACAAAC
1 CACAAAC
1481750 ACAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.59, C:0.29, G:0.09, T:0.03
Consensus pattern (13 bp):
CACAAACGAACAA
Found at i:1485849 original size:17 final size:18
Alignment explanation
Indices: 1485822--1485859 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1485812 CTTTGATGGT
1485822 TTAATTATTTTTAAATCA
1 TTAATTATTTTTAAATCA
*
1485840 TTAA-TATTTTTAAATTA
1 TTAATTATTTTTAAATCA
1485857 TTA
1 TTA
1485860 TAATTAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAATTATTTTTAAATCA
Done.