Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 58 of 135
Found at i:16794254 original size:36 final size:37
Alignment explanation
Indices: 16794214--16794288 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 37
16794204 AAAAATTTAC
* *
16794214 TTGTATCTAAAAATACCAAT-AAG-ACATTAAGTTCAA
1 TTGTAACTAAAAATACCAATAAAGCA-ATGAAGTTCAA
**
16794250 TTGTAACTTTAAATACCAATAAAGCAATGAAGTTCAA
1 TTGTAACTAAAAATACCAATAAAGCAATGAAGTTCAA
16794287 TT
1 TT
16794289 AAAACAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 17 0.52
37 15 0.45
38 1 0.03
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (37 bp):
TTGTAACTAAAAATACCAATAAAGCAATGAAGTTCAA
Found at i:16795966 original size:20 final size:20
Alignment explanation
Indices: 16795943--16795991 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
16795933 TTTTTCATGT
* *
16795943 GTATTGATATTTTTATAAA-A
1 GTATCGATAATTTTA-AAACA
16795963 GTATCGATAATTTTAAAACA
1 GTATCGATAATTTTAAAACA
16795983 GTATCGATA
1 GTATCGATA
16795992 CCAAATTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (20 bp):
GTATCGATAATTTTAAAACA
Found at i:16796514 original size:23 final size:23
Alignment explanation
Indices: 16796483--16796529 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
16796473 AAGGTATCTA
16796483 TATAATTTAGAACTATTTCACCT
1 TATAATTTAGAACTATTTCACCT
*
16796506 TATACTTTAGAACTATTTCACCT
1 TATAATTTAGAACTATTTCACCT
16796529 T
1 T
16796530 TTTGGGCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (23 bp):
TATAATTTAGAACTATTTCACCT
Found at i:16801893 original size:20 final size:20
Alignment explanation
Indices: 16801865--16801920 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
16801855 TGAAATTCTA
* *
16801865 AAATTATTTTGACTTGGTTG
1 AAATCATTTTGACTTGGTTC
** *
16801885 AAATCATTTTGTTTTGTTTC
1 AAATCATTTTGACTTGGTTC
*
16801905 AAATCATTTTAACTTG
1 AAATCATTTTGACTTG
16801921 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (20 bp):
AAATCATTTTGACTTGGTTC
Found at i:16802679 original size:26 final size:26
Alignment explanation
Indices: 16802650--16802699 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
16802640 ATTGTCATCA
16802650 TTTTATCCACATCCACATCGTCACCT
1 TTTTATCCACATCCACATCGTCACCT
16802676 TTTTATCCACATCCACATCGTCAC
1 TTTTATCCACATCCACATCGTCAC
16802700 TAGAATCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.38, G:0.04, T:0.34
Consensus pattern (26 bp):
TTTTATCCACATCCACATCGTCACCT
Found at i:16806069 original size:40 final size:40
Alignment explanation
Indices: 16806011--16806420 Score: 211
Period size: 40 Copynumber: 9.8 Consensus size: 40
16806001 TTTGGACAGA
* * *
16806011 AAACGCCACAAAAAGTAAAGCAATAGCGGTGTTTTTCAAT
1 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTCAAT
* * * *
16806051 AAACGCCGCAAAAGGTAAAGTAATAGTGGCGTTTTCCTAT
1 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTCAAT
* * * **
16806091 AAACGTCGCAAAAGGTAAAGTAATAGCGACGTTTATGGGAA-
1 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTT-T-TCAAT
* * * **
16806132 AAACACCGCCAAAGGTAAACAACAATAGCGGCGTTTATGGAA-
1 AAACGCCGCAAAAGGT-AA-AGCAATAGCGGCGTTT-TTCAAT
*
16806174 AAACACCGCAAAAGGTAAAGCAATAGCGGCGTTTTATC-AT
1 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTT-TCAAT
** * * *
16806214 AAACGCCACTATTGCCACAAAAGGTAAAGAGCAATAGCAACATTTATGAA-
1 AAACG-C-C----G---CAAAAGGT-AA-AGCAATAGCGGCGTTTTTCAAT
* * * *
16806264 AAACCACCACAAAATGTAAAGCAATAGCGGTGTTTTATC-AT
1 AAA-CGCCGCAAAAGGTAAAGCAATAGCGGCGTTTT-TCAAT
* * * **
16806305 AAAAGCTGGAAAAGGTAAAGAGCAATAGCGGCGTTTATGGAA-
1 AAACGCCGCAAAAGGT-AA-AGCAATAGCGGCGTTT-TTCAAT
* ** * * *
16806347 AAAAGCCGCAAAAGGTAAAGTTATAGCGGGGTTTTACCAT
1 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTCAAT
** *
16806387 AAACTTCGCAAAATGTAAAGCAATAGCGGCGTTT
1 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTT
16806421 ATGGATAAAA
Statistics
Matches: 282, Mismatches: 62, Indels: 52
0.71 0.16 0.13
Matches are distributed among these distances:
39 4 0.01
40 143 0.51
41 27 0.10
42 59 0.21
43 17 0.06
46 1 0.00
49 9 0.03
50 7 0.02
51 15 0.05
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.20
Consensus pattern (40 bp):
AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTCAAT
Found at i:16806188 original size:42 final size:41
Alignment explanation
Indices: 16806097--16806207 Score: 152
Period size: 42 Copynumber: 2.7 Consensus size: 41
16806087 CTATAAACGT
** *
16806097 CGCAAAAGGTAAAGTAATAGCGACGTTTATGGGAAAAACAC
1 CGCAAAAGGTAAAACAATAGCGGCGTTTATGGGAAAAACAC
*
16806138 CGCCAAAGGTAAACAACAATAGCGGCGTTTAT-GGAAAAACAC
1 CGCAAAAGGT-AA-AACAATAGCGGCGTTTATGGGAAAAACAC
*
16806180 CGCAAAAGGTAAAGCAATAGCGGCGTTT
1 CGCAAAAGGTAAAACAATAGCGGCGTTT
16806208 TATCATAAAC
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
40 15 0.24
41 11 0.18
42 21 0.34
43 15 0.24
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.16
Consensus pattern (41 bp):
CGCAAAAGGTAAAACAATAGCGGCGTTTATGGGAAAAACAC
Found at i:16806299 original size:91 final size:91
Alignment explanation
Indices: 16806142--16806307 Score: 244
Period size: 91 Copynumber: 1.8 Consensus size: 91
16806132 AAACACCGCC
** * *
16806142 AAAGGTAAACAACAATAGCGGCGTTTATGGAAAAACACCGCAAAAGGTAAAGCAATAGCGGCGTT
1 AAAGGTAAACAACAATAGCAACATTTATGGAAAAACACCACAAAAGGTAAAGCAATAGCGGCGTT
16806207 TTATCATAAACGCCACTATTGCCACA
66 TTATCATAAACGCCACTATTGCCACA
* * * *
16806233 AAAGGTAAAGAGCAATAGCAACATTTAT-GAAAAACCACCACAAAATGTAAAGCAATAGCGGTGT
1 AAAGGTAAACAACAATAGCAACATTTATGGAAAAA-CACCACAAAAGGTAAAGCAATAGCGGCGT
16806297 TTTATCATAAA
65 TTTATCATAAA
16806308 AGCTGGAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
90 6 0.09
91 60 0.91
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (91 bp):
AAAGGTAAACAACAATAGCAACATTTATGGAAAAACACCACAAAAGGTAAAGCAATAGCGGCGTT
TTATCATAAACGCCACTATTGCCACA
Found at i:16806330 original size:42 final size:42
Alignment explanation
Indices: 16806231--16806456 Score: 123
Period size: 40 Copynumber: 5.5 Consensus size: 42
16806221 ACTATTGCCA
** * *
16806231 CAAAAGGTAAAGAGCAATAGCAACATTTATG-AAAAACCA-CCA
1 CAAAAGGTAAAGAGCAATAGCGGCGTTTATGCAAAAA--AGCCG
* * * *
16806273 CAAAATGT-AA-AGCAATAGCGGTGTTTTAT-CATAAAAGCTG
1 CAAAAGGTAAAGAGCAATAGCGGCG-TTTATGCAAAAAAGCCG
* *
16806313 GAAAAGGTAAAGAGCAATAGCGGCGTTTATGGAAAAAAGCCG
1 CAAAAGGTAAAGAGCAATAGCGGCGTTTATGCAAAAAAGCCG
** * * * *
16806355 CAAAAGGT-AA-AGTTATAGCGGGGTTT-TACCATAAA-CTTCG
1 CAAAAGGTAAAGAGCAATAGCGGCGTTTATGCAAAAAAGC--CG
* * * *
16806395 CAAAATGT-AA-AGCAATAGCGGCGTTTATGGATAAAATGTCG
1 CAAAAGGTAAAGAGCAATAGCGGCGTTTATGCA-AAAAAGCCG
* *
16806436 CAAAATGTAAAGAGCATTAGC
1 CAAAAGGTAAAGAGCAATAGC
16806457 AGTGTTTTTT
Statistics
Matches: 138, Mismatches: 33, Indels: 25
0.70 0.17 0.13
Matches are distributed among these distances:
38 1 0.01
39 6 0.04
40 53 0.38
41 31 0.22
42 39 0.28
43 8 0.06
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.21
Consensus pattern (42 bp):
CAAAAGGTAAAGAGCAATAGCGGCGTTTATGCAAAAAAGCCG
Found at i:16806373 original size:82 final size:82
Alignment explanation
Indices: 16806231--16806447 Score: 230
Period size: 82 Copynumber: 2.7 Consensus size: 82
16806221 ACTATTGCCA
** * *
16806231 CAAAAGGTAAAGAGCAATAGCAACATTTAT-GAAAAACCA-CCACAAAATGTAAAGCAATAGCGG
1 CAAAAGGTAAAGAGCAATAGCGGCGTTTATGGAAAAA--AGCCGCAAAATGTAAAGCAATAGCGG
* *
16806294 TGTTTTATCATAAAAGC-T-G
64 GGTTTTACCAT-AAA-CTTCG
* * **
16806313 GAAAAGGTAAAGAGCAATAGCGGCGTTTATGGAAAAAAGCCGCAAAAGGTAAAGTTATAGCGGGG
1 CAAAAGGTAAAGAGCAATAGCGGCGTTTATGGAAAAAAGCCGCAAAATGTAAAGCAATAGCGGGG
16806378 TTTTACCATAAACTTCG
66 TTTTACCATAAACTTCG
* * *
16806395 CAAAATGT-AA-AGCAATAGCGGCGTTTATGGATAAAATGTCGCAAAATGTAAAG
1 CAAAAGGTAAAGAGCAATAGCGGCGTTTATGGA-AAAAAGCCGCAAAATGTAAAG
16806448 AGCATTAGCA
Statistics
Matches: 115, Mismatches: 15, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
80 22 0.19
81 25 0.22
82 62 0.54
83 6 0.05
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (82 bp):
CAAAAGGTAAAGAGCAATAGCGGCGTTTATGGAAAAAAGCCGCAAAATGTAAAGCAATAGCGGGG
TTTTACCATAAACTTCG
Found at i:16806429 original size:40 final size:40
Alignment explanation
Indices: 16806273--16806447 Score: 140
Period size: 40 Copynumber: 4.3 Consensus size: 40
16806263 AAAACCACCA
* *
16806273 CAAAATGTAAAGCAATAGCGGTGTTTTAT-CATAAAA-GCTG
1 CAAAATGTAAAGCAATAGCGGCG-TTTATGCATAAAATTC-G
* * * * **
16806313 GAAAAGGTAAAGAGCAATAGCGGCGTTTATGGAAAAAAGCCG
1 CAAAATGT-AA-AGCAATAGCGGCGTTTATGCATAAAATTCG
* ** * * *
16806355 CAAAAGGTAAAGTTATAGCGGGGTTT-TACCATAAACTTCG
1 CAAAATGTAAAGCAATAGCGGCGTTTAT-GCATAAAATTCG
*
16806395 CAAAATGTAAAGCAATAGCGGCGTTTATGGATAAAATGTCG
1 CAAAATGTAAAGCAATAGCGGCGTTTATGCATAAAAT-TCG
16806436 CAAAATGTAAAG
1 CAAAATGTAAAG
16806448 AGCATTAGCA
Statistics
Matches: 105, Mismatches: 23, Indels: 13
0.74 0.16 0.09
Matches are distributed among these distances:
39 1 0.01
40 53 0.50
41 25 0.24
42 25 0.24
43 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.23
Consensus pattern (40 bp):
CAAAATGTAAAGCAATAGCGGCGTTTATGCATAAAATTCG
Found at i:16808114 original size:41 final size:40
Alignment explanation
Indices: 16808058--16808194 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 40
16808048 GATAAAGAGC
* * *
16808058 AATAGTGGCGTTTATGGAAAAAATACCGCTAAAGGTTAAGT
1 AATAGCGGCGTTTATGG-AAAAACACCGCTAAAGGTTAAGA
* * * * *
16808099 ACTAGCGGCGCTTATGGAAAAACGCCGCAAAAGGTAAAGA
1 AATAGCGGCGTTTATGGAAAAACACCGCTAAAGGTTAAGA
* *
16808139 GAATTAGAGGCGTTTATGGGAAAAACACCGCTAAAGGTTAAGC
1 -AA-TAGCGGCGTTTAT-GGAAAAACACCGCTAAAGGTTAAGA
16808182 AATAGCGGCGTTT
1 AATAGCGGCGTTT
16808195 TCCCATAAAC
Statistics
Matches: 77, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
40 18 0.23
41 25 0.32
42 13 0.17
43 21 0.27
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (40 bp):
AATAGCGGCGTTTATGGAAAAACACCGCTAAAGGTTAAGA
Found at i:16808128 original size:83 final size:83
Alignment explanation
Indices: 16808035--16808191 Score: 235
Period size: 83 Copynumber: 1.9 Consensus size: 83
16808025 ATTTTTCTAT
* * * *
16808035 AAACGTCGCAAAAGATAAAGAGCAA-TAGTGGCGTTTATGGAAAAAATACCGCTAAAGGTTAAGT
1 AAACGCCGCAAAAGATAAAGAG-AATTAGAGGCGTTTATGGAAAAAACACCGCTAAAGGTTAAGC
*
16808099 ACTAGCGGCGCTTATGGAA
65 AATAGCGGCGCTTATGGAA
* *
16808118 AAACGCCGCAAAAGGTAAAGAGAATTAGAGGCGTTTATGGGAAAAACACCGCTAAAGGTTAAGCA
1 AAACGCCGCAAAAGATAAAGAGAATTAGAGGCGTTTATGGAAAAAACACCGCTAAAGGTTAAGCA
16808183 ATAGCGGCG
66 ATAGCGGCG
16808192 TTTTCCCATA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
82 2 0.03
83 64 0.97
ACGTcount: A:0.40, C:0.15, G:0.27, T:0.18
Consensus pattern (83 bp):
AAACGCCGCAAAAGATAAAGAGAATTAGAGGCGTTTATGGAAAAAACACCGCTAAAGGTTAAGCA
ATAGCGGCGCTTATGGAA
Found at i:16808162 original size:43 final size:42
Alignment explanation
Indices: 16808041--16808194 Score: 134
Period size: 43 Copynumber: 3.7 Consensus size: 42
16808031 CTATAAACGT
* * * *
16808041 CGCAAAAGATAAAGAGCAATAGTGGCGTTTATGGAAAAAATAC
1 CGCAAAAGGTAAAGAG-AATAGAGGCGTTTATGGGAAAAACAC
* * * * * * *
16808084 CGCTAAAGGTTAAG-TACTAGCGGCGCTTAT-GGAAAAACGC
1 CGCAAAAGGTAAAGAGAATAGAGGCGTTTATGGGAAAAACAC
16808124 CGCAAAAGGTAAAGAGAATTAGAGGCGTTTATGGGAAAAACAC
1 CGCAAAAGGTAAAGAGAA-TAGAGGCGTTTATGGGAAAAACAC
* * * *
16808167 CGCTAAAGGTTAAG-CAATAGCGGCGTTT
1 CGCAAAAGGTAAAGAGAATAGAGGCGTTT
16808195 TCCCATAAAC
Statistics
Matches: 87, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
40 19 0.22
41 23 0.26
42 13 0.15
43 32 0.37
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (42 bp):
CGCAAAAGGTAAAGAGAATAGAGGCGTTTATGGGAAAAACAC
Found at i:16811070 original size:28 final size:28
Alignment explanation
Indices: 16811015--16811087 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 28
16811005 TTCACTAACT
*
16811015 ATTTAATTATTTAA-T-TTAAAATATTA
1 ATTTAAATATTTAATTATTAAAATATTA
16811041 ATAATTAAATATTTAATTATTAAAA-A-TA
1 AT--TTAAATATTTAATTATTAAAATATTA
**
16811069 ATCCAAATATTTAATTATT
1 ATTTAAATATTTAATTATT
16811088 TAATTATCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 17 0.43
28 15 0.38
29 2 0.05
30 6 0.15
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTAAATATTTAATTATTAAAATATTA
Found at i:16811093 original size:34 final size:30
Alignment explanation
Indices: 16811014--16811094 Score: 85
Period size: 34 Copynumber: 2.6 Consensus size: 30
16811004 GTTCACTAAC
*
16811014 TATTTAATTATTTAA-T-TTAAAATATTAA
1 TATTTAATTATTTAATTATTAAAATATAAA
* *
16811042 TAATTAAATATTTAATTATTAAAAATAATCCAAA
1 TATTTAATTATTTAATTATT-AAAAT-AT--AAA
16811076 TATTTAATTATTTAATTAT
1 TATTTAATTATTTAATTAT
16811095 CTAATGATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
28 13 0.31
29 1 0.02
30 2 0.05
31 5 0.12
32 2 0.05
34 19 0.45
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
TATTTAATTATTTAATTATTAAAATATAAA
Found at i:16811128 original size:8 final size:8
Alignment explanation
Indices: 16811115--16811153 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
16811105 AAAACAACCC
*
16811115 AATTATTG
1 AATTATTT
16811123 AATTATTT
1 AATTATTT
*
16811131 CATTATTT
1 AATTATTT
*
16811139 CATTATTT
1 AATTATTT
16811147 AATTATT
1 AATTATT
16811154 AAAAACAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (8 bp):
AATTATTT
Found at i:16811130 original size:50 final size:50
Alignment explanation
Indices: 16811076--16811190 Score: 167
Period size: 50 Copynumber: 2.3 Consensus size: 50
16811066 ATAATCCAAA
* *
16811076 TATTTAATTATTTAATTATCTAATGATTTAAAACAACCCAATTATTGAAT
1 TATTTAATTATTTAATTATCTAATGATTAAAAACAACCCAAATATTGAAT
* * * * *
16811126 TATTTCATTATTTCATTATTTAATTATTAAAAACAACCCAAATATTTAAT
1 TATTTAATTATTTAATTATCTAATGATTAAAAACAACCCAAATATTGAAT
16811176 TATTTAATTATTTAA
1 TATTTAATTATTTAA
16811191 AACAACTCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.47
Consensus pattern (50 bp):
TATTTAATTATTTAATTATCTAATGATTAAAAACAACCCAAATATTGAAT
Found at i:16811147 original size:42 final size:42
Alignment explanation
Indices: 16811033--16811232 Score: 131
Period size: 42 Copynumber: 4.8 Consensus size: 42
16811023 ATTTAATTTA
* * * * *
16811033 AAATATT-AA-TAATTAAATATTTAATTATTAAAAATAATCC
1 AAATATTGAATTATTTAATTATTTAATTATTTAAAACAACCC
* * *
16811073 AAATATTTAATTATTTAATTATCTAATGATTTAAAACAACCC
1 AAATATTGAATTATTTAATTATTTAATTATTTAAAACAACCC
* * * **
16811115 AATTATTGAATTATTTCATTATTTCATTATTTAATTATTAA---
1 AAATATTGAATTATTTAATTATTTAATTATTTAA--AACAACCC
* *** * *
16811156 AAACAACCCAAATATTTAATTATTTAATTATTTAAAACAACTC
1 AAA-TATTGAATTATTTAATTATTTAATTATTTAAAACAACCC
* * **
16811199 AATTATTGAATTATTGAATTATCGAATTATTTAA
1 AAATATTGAATTATTTAATTATTTAATTATTTAA
16811233 TTATTTAATT
Statistics
Matches: 118, Mismatches: 34, Indels: 14
0.71 0.20 0.08
Matches are distributed among these distances:
40 10 0.08
41 4 0.03
42 99 0.84
43 2 0.02
44 3 0.03
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (42 bp):
AAATATTGAATTATTTAATTATTTAATTATTTAAAACAACCC
Found at i:16811178 original size:34 final size:34
Alignment explanation
Indices: 16811134--16811268 Score: 128
Period size: 34 Copynumber: 4.3 Consensus size: 34
16811124 ATTATTTCAT
*
16811134 TATTTCATTATTTAATTATTAAAAACAACCCAAA
1 TATTTAATTATTTAATTATTAAAAACAACCCAAA
* * *
16811168 TATTTAATTATTTAATTATTTAAAACAACTCAAT
1 TATTTAATTATTTAATTATTAAAAACAACCCAAA
* * * *
16811202 TATTGAATTATTGAATTA-T---------CGAAT
1 TATTTAATTATTTAATTATTAAAAACAACCCAAA
16811226 TATTTAATTATTTAATTATTAAAAACAACCCAAA
1 TATTTAATTATTTAATTATTAAAAACAACCCAAA
16811260 TATTTAATT
1 TATTTAATT
16811269 CAAAATATTT
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
24 19 0.24
25 1 0.01
33 1 0.01
34 58 0.73
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (34 bp):
TATTTAATTATTTAATTATTAAAAACAACCCAAA
Found at i:16811181 original size:8 final size:8
Alignment explanation
Indices: 16811168--16811245 Score: 66
Period size: 8 Copynumber: 9.5 Consensus size: 8
16811158 ACAACCCAAA
16811168 TATTTAAT
1 TATTTAAT
16811176 TATTTAAT
1 TATTTAAT
*
16811184 TATTTAAAAC
1 TATTT--AAT
* * *
16811194 AACTCAAT
1 TATTTAAT
*
16811202 TATTGAAT
1 TATTTAAT
*
16811210 TATTGAAT
1 TATTTAAT
**
16811218 TATCGAAT
1 TATTTAAT
16811226 TATTTAAT
1 TATTTAAT
16811234 TATTTAAT
1 TATTTAAT
16811242 TATT
1 TATT
16811246 AAAAACAACC
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
8 53 0.93
10 4 0.07
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (8 bp):
TATTTAAT
Found at i:16811234 original size:24 final size:24
Alignment explanation
Indices: 16811199--16811244 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
16811189 AAAACAACTC
16811199 AATTATTGAATTATTGAATTATCG
1 AATTATTGAATTATTGAATTATCG
* *
16811223 AATTATTTAATTATTTAATTAT
1 AATTATTGAATTATTGAATTAT
16811245 TAAAAACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (24 bp):
AATTATTGAATTATTGAATTATCG
Found at i:16811276 original size:14 final size:13
Alignment explanation
Indices: 16811256--16811322 Score: 55
Period size: 14 Copynumber: 5.0 Consensus size: 13
16811246 AAAAACAACC
16811256 CAAATATTTAATT
1 CAAATATTTAATT
16811269 CAAAATATTTAATT
1 C-AAATATTTAATT
** * *
16811283 -ATTTAATTCAACT
1 CAAAT-ATTTAATT
*
16811296 CAATTATTTAATT
1 CAAATATTTAATT
16811309 CAAAATATTTAATT
1 C-AAATATTTAATT
16811323 ATTAAAAACA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
12 2 0.05
13 14 0.33
14 26 0.62
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (13 bp):
CAAATATTTAATT
Found at i:16811278 original size:40 final size:40
Alignment explanation
Indices: 16811234--16811352 Score: 175
Period size: 40 Copynumber: 3.0 Consensus size: 40
16811224 ATTATTTAAT
*
16811234 TATTTAATTATTAAAAACAACCCAAATATTTAATTCAAAA
1 TATTTAATTATTAAAAACAACTCAAATATTTAATTCAAAA
* ** *
16811274 TATTTAATTATTTAATTCAACTCAATTATTTAATTCAAAA
1 TATTTAATTATTAAAAACAACTCAAATATTTAATTCAAAA
**
16811314 TATTTAATTATTAAAAACAACTCAAATATTCGATTCAAA
1 TATTTAATTATTAAAAACAACTCAAATATTTAATTCAAA
16811353 TTAAAATTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (40 bp):
TATTTAATTATTAAAAACAACTCAAATATTTAATTCAAAA
Found at i:16817190 original size:42 final size:43
Alignment explanation
Indices: 16817110--16817205 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 43
16817100 CTGTTAATGT
*
16817110 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGACCATGTTCTA
* * *
16817153 TAGCGGAGTTTGTTGG-AAAGCACCGCTAAAGATCATGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGACCATGTTCTA
16817195 TAGCGGCGTTT
1 TAGCGGCGTTT
16817206 TACTCATAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 34 0.71
43 14 0.29
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGACCATGTTCTA
Found at i:16817243 original size:34 final size:33
Alignment explanation
Indices: 16817195--16817263 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 33
16817185 TCATGTTCTA
* *
16817195 TAGCGGCGTTTTACTCATAAACGCTGCAAGTTT
1 TAGCAGCGTTTTACTCATAAACGCCGCAAGTTT
* *
16817228 TAGCAGCGTTTTTACTCATAAATGCCGCGAGTTT
1 TAGCAGCG-TTTTACTCATAAACGCCGCAAGTTT
16817262 TA
1 TA
16817264 ACGGCACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 7 0.23
34 24 0.77
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (33 bp):
TAGCAGCGTTTTACTCATAAACGCCGCAAGTTT
Found at i:16817275 original size:34 final size:34
Alignment explanation
Indices: 16817203--16817275 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
16817193 TATAGCGGCG
* * **
16817203 TTTTACTCATAAACGCTGCAAGTTTTAGCAGCGT
1 TTTTACTCATAAACGCCGCAAGTTTTAACAGCAC
* * *
16817237 TTTTACTCATAAATGCCGCGAGTTTTAACGGCAC
1 TTTTACTCATAAACGCCGCAAGTTTTAACAGCAC
16817271 TTTTA
1 TTTTA
16817276 GGGCCAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (34 bp):
TTTTACTCATAAACGCCGCAAGTTTTAACAGCAC
Found at i:16818612 original size:23 final size:23
Alignment explanation
Indices: 16818584--16819053 Score: 607
Period size: 23 Copynumber: 20.3 Consensus size: 23
16818574 TGTTCATCTA
*
16818584 TGCTTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
* * *
16818607 TGCTTAAATATTTATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
16818630 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
16818653 TGCTTAAGTATTAATGGGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
16818676 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
16818699 TGCTCAAAAATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
16818722 TACTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
16818745 TACTCAAATATTAAAGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
16818768 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
16818791 TGCTTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
16818814 TACTTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
16818837 TACTTAAATATTAATGTAATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
16818860 TACTTAAATATTAAAGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
16818883 TGTTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
16818906 TGCTCAAATATTAAAGTGTGATTTG
1 TGCTTAAATATT-AA-TGTGATTTG
* *
16818931 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
16818954 TGCTTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
16818977 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
16819000 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
16819023 TGATTAAATATTAATGCGATTTG
1 TGCTTAAATATTAATGTGATTTG
16819046 TGCTTAAA
1 TGCTTAAA
16819054 GAATTAAGAT
Statistics
Matches: 393, Mismatches: 52, Indels: 4
0.88 0.12 0.01
Matches are distributed among these distances:
23 369 0.94
24 4 0.01
25 20 0.05
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:16819236 original size:36 final size:36
Alignment explanation
Indices: 16819132--16819236 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
16819122 TTGTGAAAGT
* *
16819132 AAATATGTGGGTATGTTCTTCATGTCATGTGACAGA
1 AAATATGTGGGTATGTTCTTCATGCCATGTGACAAA
* *
16819168 AAATATATGGGTATGTTTTTCATGCCATGTGACAAA
1 AAATATGTGGGTATGTTCTTCATGCCATGTGACAAA
16819204 AAATATGTGGGTATGTTCTTCATGCCATGTGAC
1 AAATATGTGGGTATGTTCTTCATGCCATGTGAC
16819237 TAATTATATT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (36 bp):
AAATATGTGGGTATGTTCTTCATGCCATGTGACAAA
Found at i:16821642 original size:14 final size:14
Alignment explanation
Indices: 16821604--16821645 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
16821594 TTATAAAAAA
*
16821604 AAATTAATTTTATT
1 AAATAAATTTTATT
*
16821618 AAA-ATATTTTATT
1 AAATAAATTTTATT
16821631 AAATAAATTTTATT
1 AAATAAATTTTATT
16821645 A
1 A
16821646 TCATTTATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATAAATTTTATT
Found at i:16822420 original size:15 final size:17
Alignment explanation
Indices: 16822397--16822428 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16822387 TGCTTTGTTG
16822397 TTTTACAC-TTTCTTTA
1 TTTTACACTTTTCTTTA
16822413 TTTT-CACTTTTCTTTA
1 TTTTACACTTTTCTTTA
16822429 CCTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTACACTTTTCTTTA
Found at i:16822446 original size:24 final size:27
Alignment explanation
Indices: 16822398--16822448 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 27
16822388 GCTTTGTTGT
16822398 TTTACACTTTCTTTATTTTCACTTTTC
1 TTTACACTTTCTTTATTTTCACTTTTC
*
16822425 TTTAC-CTTT-TTT-TTTTCTCTTTTC
1 TTTACACTTTCTTTATTTTCACTTTTC
16822449 ACATATAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 11 0.48
25 3 0.13
26 4 0.17
27 5 0.22
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTACACTTTCTTTATTTTCACTTTTC
Found at i:16826292 original size:4 final size:4
Alignment explanation
Indices: 16826283--16826309 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
16826273 ACAAAATAAA
16826283 ACAG ACAG ACAG ACAG ACAG ACAG ACA
1 ACAG ACAG ACAG ACAG ACAG ACAG ACA
16826310 AAACATAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.22, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:16831423 original size:67 final size:68
Alignment explanation
Indices: 16831307--16831441 Score: 236
Period size: 67 Copynumber: 2.0 Consensus size: 68
16831297 TTGGAAACTC
* *
16831307 AATCAAGAAAAAGTACTAAACTGTAATTATGACAAAAAGTCATATAAATCTTACACTCACATTTT
1 AATCAAGAAAAAGTACTAAACTGTAATTATGACAAAAAGCCATACAAATCTTACACTCACATTTT
16831372 CTT
66 CTT
*
16831375 AATCAAGAAAAA-TACTAAACTGTAATTATGACAAAAAGCCATGCAAATCTTACACTCACATTTT
1 AATCAAGAAAAAGTACTAAACTGTAATTATGACAAAAAGCCATACAAATCTTACACTCACATTTT
16831439 CTT
66 CTT
16831442 TCTGCAAGCA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
67 52 0.81
68 12 0.19
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (68 bp):
AATCAAGAAAAAGTACTAAACTGTAATTATGACAAAAAGCCATACAAATCTTACACTCACATTTT
CTT
Found at i:16843327 original size:35 final size:35
Alignment explanation
Indices: 16843281--16843350 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
16843271 TATCATAAGC
16843281 ATCCTTATCTTTCTTCTCCAATGCTGAACATAGTT
1 ATCCTTATCTTTCTTCTCCAATGCTGAACATAGTT
* *
16843316 ATCCTTATCTTTCTTCTCCAGTGCTGACCATAGTT
1 ATCCTTATCTTTCTTCTCCAATGCTGAACATAGTT
16843351 CCTCCCACTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.10, T:0.43
Consensus pattern (35 bp):
ATCCTTATCTTTCTTCTCCAATGCTGAACATAGTT
Found at i:16851901 original size:51 final size:52
Alignment explanation
Indices: 16851823--16852060 Score: 286
Period size: 51 Copynumber: 4.6 Consensus size: 52
16851813 GTGGGATTTG
* ** *
16851823 TATACTCACGATCACACAGAGTCATCGGACCTCTT-AATCCGTAAAGGA-TCA
1 TATACTCACGATGACACTTAGTCATCGGACCT-TTAAATCCATAAAGGATTCA
* *
16851874 TATACTCACGATGGCACTTAGTAATCGGACCTTTAAATCCATAAAGGATTCA
1 TATACTCACGATGACACTTAGTCATCGGACCTTTAAATCCATAAAGGATTCA
* *
16851926 TATACTCACAATGACACTTAGTCATCGAACCTTTAAATCCATAAAGGATTTCA
1 TATACTCACGATGACACTTAGTCATCGGACCTTTAAATCCATAAAGGA-TTCA
* * * * **
16851979 TAAACTCACGATGACACTTAGTCATTGAACC-TCATAATCTGTAAAGGATT-A
1 TATACTCACGATGACACTTAGTCATCGGACCTTTA-AATCCATAAAGGATTCA
*
16852030 TTTACTCACGATGACACTTAGTCATCGGACC
1 TATACTCACGATGACACTTAGTCATCGGACC
16852061 CTTTTTCATT
Statistics
Matches: 163, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
50 2 0.01
51 67 0.41
52 51 0.31
53 43 0.26
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (52 bp):
TATACTCACGATGACACTTAGTCATCGGACCTTTAAATCCATAAAGGATTCA
Found at i:16851999 original size:53 final size:52
Alignment explanation
Indices: 16851766--16852056 Score: 286
Period size: 52 Copynumber: 5.6 Consensus size: 52
16851756 ATTTCACTTC
* * * * ****
16851766 ATTCATATACTCACGATGACACATAGCCACCAAACC-TTATAATCCACGTGGG
1 ATTCATATACTCACGATGACACTTAGTCATCGAACCTTTA-AATCCATAAAGG
** * ** * *
16851818 ATTTGTATACTCACGATCACACAGAGTCATCGGACCTCTT-AATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGAACCT-TTAAATCCATAAAGG
* * *
16851870 A-TCATATACTCACGATGGCACTTAGTAATCGGACCTTTAAATCCATAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGAACCTTTAAATCCATAAAGG
*
16851921 ATTCATATACTCACAATGACACTTAGTCATCGAACCTTTAAATCCATAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGAACCTTTAAATCCATAAAGG
* * * **
16851973 ATTTCATAAACTCACGATGACACTTAGTCATTGAACC-TCATAATCTGTAAAGG
1 A-TTCATATACTCACGATGACACTTAGTCATCGAACCTTTA-AATCCATAAAGG
*
16852026 ATT-ATTTACTCACGATGACACTTAGTCATCG
1 ATTCATATACTCACGATGACACTTAGTCATCG
16852057 GACCCTTTTT
Statistics
Matches: 199, Mismatches: 34, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
50 2 0.01
51 65 0.33
52 87 0.44
53 43 0.22
54 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGTCATCGAACCTTTAAATCCATAAAGG
Found at i:16861531 original size:34 final size:34
Alignment explanation
Indices: 16861471--16861559 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
16861461 TATTTAATTT
*
16861471 TTGGTGAGCTCGCATCTTTTGGTGAGCTCACAATC
1 TTGGTGAGCTCGCA-CATTTGGTGAGCTCACAATC
*** * *
16861506 TTGGTGAGCTCGCACATTTGGTGAGCTTGTAGTT
1 TTGGTGAGCTCGCACATTTGGTGAGCTCACAATC
*
16861540 TTGGTGAGCTCGCATATTTG
1 TTGGTGAGCTCGCACATTTG
16861560 CATTTAGTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
34 33 0.70
35 14 0.30
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (34 bp):
TTGGTGAGCTCGCACATTTGGTGAGCTCACAATC
Found at i:16861559 original size:17 final size:17
Alignment explanation
Indices: 16861470--16861559 Score: 94
Period size: 17 Copynumber: 5.2 Consensus size: 17
16861460 GTATTTAATT
*
16861470 TTTGGTGAGCTCGCATCT
1 TTTGGTGAGCTCGCAT-A
*
16861488 TTTGGTGAGCTCACA-A
1 TTTGGTGAGCTCGCATA
*
16861504 TCTTGGTGAGCTCGCACA
1 T-TTGGTGAGCTCGCATA
* *
16861522 TTTGGTGAGCTTGTAGT-
1 TTTGGTGAGCTCGCA-TA
16861539 TTTGGTGAGCTCGCATA
1 TTTGGTGAGCTCGCATA
16861556 TTTG
1 TTTG
16861560 CATTTAGTGT
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
16 2 0.03
17 42 0.70
18 16 0.27
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.38
Consensus pattern (17 bp):
TTTGGTGAGCTCGCATA
Found at i:16861843 original size:30 final size:30
Alignment explanation
Indices: 16861802--16861871 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
16861792 ATTTTCGAAA
16861802 ATTATGGGATTTAACAATTTGGGAATAAGGG
1 ATTA-GGGATTTAACAATTTGGGAATAAGGG
*
16861833 ATTAGGGATTTCACAATTTGGGAATAAGGG
1 ATTAGGGATTTAACAATTTGGGAATAAGGG
*
16861863 ATTAAGGAT
1 ATTAGGGAT
16861872 GTAGAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
30 33 0.89
31 4 0.11
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.31
Consensus pattern (30 bp):
ATTAGGGATTTAACAATTTGGGAATAAGGG
Found at i:16861945 original size:15 final size:15
Alignment explanation
Indices: 16861925--16861957 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
16861915 AAAGATTGTA
16861925 GGGATTTCACG-AATT
1 GGGATTTCA-GAAATT
16861940 GGGATTTCAGAAATT
1 GGGATTTCAGAAATT
16861955 GGG
1 GGG
16861958 GTTTTGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.06
15 16 0.94
ACGTcount: A:0.27, C:0.09, G:0.33, T:0.30
Consensus pattern (15 bp):
GGGATTTCAGAAATT
Found at i:16862071 original size:31 final size:28
Alignment explanation
Indices: 16862042--16862094 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
16862032 GGGTTTATTG
16862042 TATTTAA-TT-TTTTTGCCACATCATCT
1 TATTTAATTTATTTTTGCCACATCATCT
16862068 TATTTAATTTATTTTTGCCACATCATC
1 TATTTAATTTATTTTTGCCACATCATC
16862095 CTTCAACTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 7 0.28
27 2 0.08
28 16 0.64
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.53
Consensus pattern (28 bp):
TATTTAATTTATTTTTGCCACATCATCT
Found at i:16862439 original size:43 final size:44
Alignment explanation
Indices: 16862373--16862496 Score: 187
Period size: 43 Copynumber: 2.8 Consensus size: 44
16862363 ATTGAGTTTG
* *
16862373 TTGGATTATTTAGAATTAAGATTAAACTGATAGAATGTCTATTA
1 TTGGATTATTTAGGATTAAGATTAAATTGATAGAATGTCTATTA
* *
16862417 TTGGA-TATTTAGGATTAGGATTAAATTGATAGAATGTTTATTA
1 TTGGATTATTTAGGATTAAGATTAAATTGATAGAATGTCTATTA
* *
16862460 TTGGATTATTTAAGATTAATATTAAATTGATAGAATG
1 TTGGATTATTTAGGATTAAGATTAAATTGATAGAATG
16862497 GTTAAGTATT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 39 0.54
44 33 0.46
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.43
Consensus pattern (44 bp):
TTGGATTATTTAGGATTAAGATTAAATTGATAGAATGTCTATTA
Found at i:16868908 original size:58 final size:56
Alignment explanation
Indices: 16868763--16868909 Score: 161
Period size: 58 Copynumber: 2.5 Consensus size: 56
16868753 ATATATTATA
* * *
16868763 ATTTTTACTAATTCATATTTTAATAATACTTATATTAAAAAATATTATTAAATTACAT
1 ATTTTTATTAATT-ATA-TTTAATAATAATTATATTAAAAAATATTAATAAATTACAT
* * *
16868821 ATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTA-AT
1 A-T-TTTTATT-AATTATATTTAATAATAATTATATTAAAAAAT-ATT-AATAAATTACAT
16868881 ATTTTTATTCAATTATATTTAATAATAAT
1 ATTTTTATT-AATTATATTTAATAATAAT
16868910 CATTAAAATT
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
58 26 0.34
59 24 0.32
60 14 0.18
61 12 0.16
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (56 bp):
ATTTTTATTAATTATATTTAATAATAATTATATTAAAAAATATTAATAAATTACAT
Found at i:16869099 original size:16 final size:17
Alignment explanation
Indices: 16869078--16869149 Score: 116
Period size: 16 Copynumber: 4.5 Consensus size: 17
16869068 TGAATTACTG
16869078 ATTACAGCTT-TATTCC
1 ATTACAGCTTCTATTCC
16869094 ATTACAGC-TCTATTCC
1 ATTACAGCTTCTATTCC
16869110 ATTACAG-TTCTATTCC
1 ATTACAGCTTCTATTCC
16869126 ATTACA-CTTCTATTCC
1 ATTACAGCTTCTATTCC
16869142 ATTACAGC
1 ATTACAGC
16869150 GAACCAAACT
Statistics
Matches: 52, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.02
16 50 0.96
17 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.06, T:0.40
Consensus pattern (17 bp):
ATTACAGCTTCTATTCC
Found at i:16883495 original size:18 final size:18
Alignment explanation
Indices: 16883472--16883506 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16883462 ATGAATAATC
*
16883472 TGCAGGTAAAACAAGATT
1 TGCAGGGAAAACAAGATT
*
16883490 TGCAGGGAAAATAAGAT
1 TGCAGGGAAAACAAGAT
16883507 AGTGGTGCAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.20
Consensus pattern (18 bp):
TGCAGGGAAAACAAGATT
Found at i:16900245 original size:20 final size:20
Alignment explanation
Indices: 16900220--16900267 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
16900210 CATAATGATA
16900220 TATATAAAAATTATTTTCAT-
1 TATATAAAAATTATTTT-ATC
***
16900240 TATATATTTATTATTTTATC
1 TATATAAAAATTATTTTATC
16900260 TATATAAA
1 TATATAAA
16900268 TAAAAAAAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATAAAAATTATTTTATC
Found at i:16900307 original size:23 final size:23
Alignment explanation
Indices: 16900265--16900308 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
16900255 TTATCTATAT
*
16900265 AAATAAAAAAAGTTATTAATTAA
1 AAATAAAAAAAGTTAATAATTAA
16900288 AAATAAAAAAA-TTGAATAATT
1 AAATAAAAAAAGTT-AATAATT
16900309 TATTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (23 bp):
AAATAAAAAAAGTTAATAATTAA
Found at i:16903141 original size:13 final size:14
Alignment explanation
Indices: 16903114--16903151 Score: 60
Period size: 13 Copynumber: 2.7 Consensus size: 14
16903104 TTAAGCTAAT
16903114 AAAAATATAATCTCG
1 AAAAATA-AATCTCG
16903129 AAAAATAAA-CTCG
1 AAAAATAAATCTCG
16903142 AAAAATAAAT
1 AAAAATAAAT
16903152 TTGGGTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.59
14 2 0.09
15 7 0.32
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (14 bp):
AAAAATAAATCTCG
Found at i:16908863 original size:42 final size:42
Alignment explanation
Indices: 16908806--16908952 Score: 152
Period size: 42 Copynumber: 3.5 Consensus size: 42
16908796 TAGGCTCTAT
* * *
16908806 CGAGTCATAAGTCTTCCTTTAATTATATTCTCATTCTCATCC
1 CGAGACATGAGTCTTCCTTTAATTATATTCTCATGCTCATCC
* * *
16908848 CAAGACATGAGTCTTCCTTTAATTATATTTTCATGCTCATTC
1 CGAGACATGAGTCTTCCTTTAATTATATTCTCATGCTCATCC
* * * * * * *
16908890 CGAGCCACGAGTCTT-CTATTTATACAAATTCTCATGCTCAACT
1 CGAGACATGAGTCTTCCT-TTAAT-TATATTCTCATGCTCATCC
16908933 CGAGACATGAGTCTTCCTTT
1 CGAGACATGAGTCTTCCTTT
16908953 TTATACAACA
Statistics
Matches: 84, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
41 2 0.02
42 52 0.62
43 28 0.33
44 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTAATTATATTCTCATGCTCATCC
Found at i:16911603 original size:12 final size:13
Alignment explanation
Indices: 16911567--16911604 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
16911557 TTTAAAACTC
*
16911567 TAATTTTTAGGAT
1 TAATATTTAGGAT
16911580 TAATATTTAGGAT
1 TAATATTTAGGAT
*
16911593 TATTA-TTAGGAT
1 TAATATTTAGGAT
16911605 ATTGTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (13 bp):
TAATATTTAGGAT
Found at i:16931093 original size:38 final size:38
Alignment explanation
Indices: 16931038--16931144 Score: 135
Period size: 38 Copynumber: 2.8 Consensus size: 38
16931028 ATCTGCCTTT
* *
16931038 TATGTCACGACATGGAATGTTTGTGTCACGGCATACCC
1 TATGTCACAACATGGAATGTTTGTGTCACGACATACCC
* * *
16931076 TATGTCACAACAAGGAATATTTGTGTCAAC-ACATACCT
1 TATGTCACAACATGGAATGTTTGTGTC-ACGACATACCC
* *
16931114 TATGTCGCAACATGGAATGTTGGTGTCACGA
1 TATGTCACAACATGGAATGTTTGTGTCACGA
16931145 TAAACCCCTA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
37 2 0.03
38 54 0.93
39 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (38 bp):
TATGTCACAACATGGAATGTTTGTGTCACGACATACCC
Found at i:16935360 original size:16 final size:16
Alignment explanation
Indices: 16935339--16935370 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16935329 TGTCTAGACT
16935339 TGGTTTGCTTGAGGAC
1 TGGTTTGCTTGAGGAC
16935355 TGGTTTGCTTGAGGAC
1 TGGTTTGCTTGAGGAC
16935371 AAGCAAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.38, T:0.38
Consensus pattern (16 bp):
TGGTTTGCTTGAGGAC
Found at i:16940432 original size:13 final size:11
Alignment explanation
Indices: 16940404--16940446 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
16940394 AGTTAAATAT
16940404 TATTTTATTAA
1 TATTTTATTAA
16940415 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
16940428 TA-TTTATTAT
1 TATTTTATTAA
16940438 TATTTTATT
1 TATTTTATT
16940447 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:16940433 original size:23 final size:23
Alignment explanation
Indices: 16940407--16940450 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
16940397 TAAATATTAT
16940407 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
16940430 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
16940451 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:16954766 original size:15 final size:15
Alignment explanation
Indices: 16954748--16954788 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
16954738 GCATTGTGTT
16954748 TGTTCGCAACATGAG
1 TGTTCGCAACATGAG
16954763 TGTTCGCAACATGAG
1 TGTTCGCAACATGAG
*
16954778 TGCTCGCAACA
1 TGTTCGCAACA
16954789 CCAGTGCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (15 bp):
TGTTCGCAACATGAG
Found at i:16954769 original size:30 final size:30
Alignment explanation
Indices: 16954694--16954770 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
16954684 TCCATGCTCA
* *
16954694 CAACATCAGTGTTAGCATTGTGTGTGTTCG
1 CAACATGAGTGTTCGCATTGTGTGTGTTCG
** *
16954724 CAACATGAGCATTCGCATTGTGTTTGTTCG
1 CAACATGAGTGTTCGCATTGTGTGTGTTCG
16954754 CAACATGAGTGTTCGCA
1 CAACATGAGTGTTCGCA
16954771 ACATGAGTGC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (30 bp):
CAACATGAGTGTTCGCATTGTGTGTGTTCG
Found at i:16963731 original size:50 final size:49
Alignment explanation
Indices: 16963662--16964071 Score: 221
Period size: 50 Copynumber: 8.4 Consensus size: 49
16963652 CACACCAAAT
* * *
16963662 CTTATAGCTGTAGAGGGGCAGATTAAAG-TCGCGAATGCGAATCTTATACC
1 CTTAAAGCTGTAGAGGGGCAGATTAAAGCT-AC-AAAGCGAATCTTATACC
* * ** * *
16963712 CTTAAAGCTGTAGAAGGGCAGATTGAAGCTGTAATGGCGAATCATATACC
1 CTTAAAGCTGTAGAGGGGCAGATTAAAGCTACAA-AGCGAATCTTATACC
* * * *
16963762 CCTAAAACTGTAGAGGGGCAAATTGAAGCTACAAAAGCGAATCTTATACC
1 CTTAAAGCTGTAGAGGGGCAGATTAAAGCTAC-AAAGCGAATCTTATACC
* * * *
16963812 CTTAATA-TTGTAGAGGGGTAGATTAAAGCCACAAAGACGAATTTTATACC
1 CTTAA-AGCTGTAGAGGGGCAGATTAAAGCTACAAAG-CGAATCTTATACC
* * * *
16963862 CCTAAAGCTATAGAGGGGCAGATTGAAGCTGCAAAG-GTAA----AT---
1 CTTAAAGCTGTAGAGGGGCAGATTAAAGCTACAAAGCG-AATCTTATACC
* * * * * * *
16963904 CTTATAGCTATAGAGGGGTAGATTGAAGTTGCAAAGGCGAATCTTATGTCC
1 CTTAAAGCTGTAGAGGGGCAGATTAAAGCTACAAA-GCGAATCTTAT-ACC
* * * * * * *
16963955 C-TAAAGCTGTAAAGGGACAAATTGAAGCCACGAAGGCAAATCTTATACC
1 CTTAAAGCTGTAGAGGGGCAGATTAAAGCTAC-AAAGCGAATCTTATACC
* * * ** * * * *
16964004 CCTAAAGTTGTAAAGGGATAGATTGAAGCCACGAAGGTGAATCTTATACC
1 CTTAAAGCTGTAGAGGGGCAGATTAAAGCTAC-AAAGCGAATCTTATACC
** *
16964054 AGTAAAGCTCTAGAGGGG
1 CTTAAAGCTGTAGAGGGG
16964072 TAAATTGAAG
Statistics
Matches: 286, Mismatches: 55, Indels: 38
0.75 0.15 0.10
Matches are distributed among these distances:
42 31 0.11
43 3 0.01
44 1 0.00
45 2 0.01
47 2 0.01
48 1 0.00
49 12 0.04
50 227 0.79
51 7 0.02
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (49 bp):
CTTAAAGCTGTAGAGGGGCAGATTAAAGCTACAAAGCGAATCTTATACC
Found at i:16963853 original size:100 final size:100
Alignment explanation
Indices: 16963701--16964252 Score: 392
Period size: 100 Copynumber: 5.7 Consensus size: 100
16963691 CGCGAATGCG
* * * *** * *
16963701 AATCTTATACCCTTAAAGCTGTAGAAGGGCAGATTGAAGCTGTAATGGCGAATCATATACCCCTA
1 AATCTTATACCCTTAAAGTTGTAGAGGGGTAGATTGAAGCCACAAAGGCGAATCTTATACCCCTA
* * *
16963766 AAACTGTAGAGGGGCAAATTGAAGCTACAAAAGCG
66 AAGCTGTAGAGGGGCAAATTGAAGCTACAAAGGCA
* * *
16963801 AATCTTATACCCTTAATA-TTGTAGAGGGGTAGATTAAAGCCACAAAGACGAATTTTATACCCCT
1 AATCTTATACCCTTAA-AGTTGTAGAGGGGTAGATTGAAGCCACAAAGGCGAATCTTATACCCCT
* * * *
16963865 AAAGCTATAGAGGGGCAGATTGAAGCTGCAAAGGTA
65 AAAGCTGTAGAGGGGCAAATTGAAGCTACAAAGGCA
* *** **
16963901 AATCTTATA-GC-T--A----TAGAGGGGTAGATTGAAGTTGCAAAGGCGAATCTTATGTCCCTA
1 AATCTTATACCCTTAAAGTTGTAGAGGGGTAGATTGAAGCCACAAAGGCGAATCTTATACCCCTA
* * * *
16963958 AAGCTGTAAAGGGACAAATTGAAGCCACGAAGGCA
66 AAGCTGTAGAGGGGCAAATTGAAGCTACAAAGGCA
* * * * * **
16963993 AATCTTATACCCCTAAAGTTGTAAAGGGATAGATTGAAGCCACGAAGGTGAATCTTATACCAGTA
1 AATCTTATACCCTTAAAGTTGTAGAGGGGTAGATTGAAGCCACAAAGGCGAATCTTATACCCCTA
* *
16964058 AAGCTCTAGAGGGGTAAATTGAAGC--C----GCA
66 AAGCTGTAGAGGGGCAAATTGAAGCTACAAAGGCA
** * * * * *
16964087 AAGGTGAT--TCTTAAA-TCTCTA-AGGGGGTAGATTGAAGCCACGAAGGTGAATCTTATACCCC
1 AATCTTATACCCTTAAAGT-TGTAGA-GGGGTAGATTGAAGCCACAAAGGCGAATCTTATACCCC
* * * *
16964148 TAAAGC--T-GAGGGGCAGATTAAAGCCACGAAGGCA
64 TAAAGCTGTAGAGGGGCAAATTGAAGCTACAAAGGCA
* * * * * * * * * *
16964182 AATCTTATACCCCTAAAGCTATAGAAGGGCAAATTGAAGTCGCGAAGGCAAATCTTATACCCCCT
1 AATCTTATACCCTTAAAGTTGTAGAGGGGTAGATTGAAGCCACAAAGGCGAATCTTATA-CCCCT
16964247 AAAGCT
65 AAAGCT
16964253 ATCAAGGGTT
Statistics
Matches: 352, Mismatches: 77, Indels: 47
0.74 0.16 0.10
Matches are distributed among these distances:
89 14 0.04
90 1 0.00
91 3 0.01
92 121 0.34
93 1 0.00
94 9 0.03
95 9 0.03
96 1 0.00
97 35 0.10
98 13 0.04
99 1 0.00
100 143 0.41
101 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (100 bp):
AATCTTATACCCTTAAAGTTGTAGAGGGGTAGATTGAAGCCACAAAGGCGAATCTTATACCCCTA
AAGCTGTAGAGGGGCAAATTGAAGCTACAAAGGCA
Found at i:16963927 original size:42 final size:42
Alignment explanation
Indices: 16963867--16963950 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
16963857 ATACCCCTAA
*
16963867 AGCTATAGAGGGGCAGATTGAAGCTGCAAAGGTAAATCTTAT
1 AGCTATAGAGGGGCAGATTGAAGCTGCAAAGGCAAATCTTAT
* * *
16963909 AGCTATAGAGGGGTAGATTGAAGTTGCAAAGGCGAATCTTAT
1 AGCTATAGAGGGGCAGATTGAAGCTGCAAAGGCAAATCTTAT
16963951 GTCCCTAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.35, C:0.11, G:0.30, T:0.25
Consensus pattern (42 bp):
AGCTATAGAGGGGCAGATTGAAGCTGCAAAGGCAAATCTTAT
Found at i:16963979 original size:92 final size:92
Alignment explanation
Indices: 16963822--16964190 Score: 224
Period size: 92 Copynumber: 4.0 Consensus size: 92
16963812 CTTAATATTG
* * * *
16963822 TAGAGGGGTAGATTAAAGCCACAAAGACGAATTTTATACCCCTAAAGCTATAGAGGGGCAGATTG
1 TAGAGGGGTAGATTAAAGCCACAAAGACGAATCTTATACCCCTAAAGCTATAAAGGGACAAATTG
** *
16963887 AAGCTGCAAAGGTAAATCTTATAGCTA
66 AAGCCACAAAGGCAAATCTTATAGCTA
* *** * ** *
16963914 TAGAGGGGTAGATTGAAGTTGCAAAGGCGAATCTTATGTCCCTAAAGCTGTAAAGGGACAAATTG
1 TAGAGGGGTAGATTAAAGCCACAAAGACGAATCTTATACCCCTAAAGCTATAAAGGGACAAATTG
* *
16963979 AAGCCACGAAGGCAAATCTTATACCCCTAAA
66 AAGCCACAAAGGCAAATCTTATA--GCT--A
* * * * ** ** * * **
16964010 GTTGTAAAGGGATAGATTGAAGCCACGAAGGTGAATCTTATACCAGTAAAGCTCTAGAGGGGTAA
1 ----TAGAGGGGTAGATTAAAGCCACAAAGACGAATCTTATACCCCTAAAGCTATAAAGGGACAA
* ** * * * *
16964075 ATTGAAGCCGCAAAGGTGATTCTTAAATCTC
62 ATTGAAGCCACAAAGGCAAATCTTATAGCTA
* * ** * * *
16964106 TA-AGGGGGTAGATTGAAGCCACGAAGGTGAATCTTATACCCCTAAAGC--T-GAGGGGCAGATT
1 TAGA-GGGGTAGATTAAAGCCACAAAGACGAATCTTATACCCCTAAAGCTATAAAGGGACAAATT
* *
16964167 AAAGCCACGAAGGCAAATCTTATA
65 GAAGCCACAAAGGCAAATCTTATA
16964191 CCCCTAAAGC
Statistics
Matches: 216, Mismatches: 52, Indels: 21
0.75 0.18 0.07
Matches are distributed among these distances:
89 27 0.12
90 1 0.00
91 1 0.00
92 115 0.53
94 2 0.01
96 1 0.00
98 2 0.01
100 67 0.31
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (92 bp):
TAGAGGGGTAGATTAAAGCCACAAAGACGAATCTTATACCCCTAAAGCTATAAAGGGACAAATTG
AAGCCACAAAGGCAAATCTTATAGCTA
Found at i:16964035 original size:192 final size:191
Alignment explanation
Indices: 16963712--16964199 Score: 552
Period size: 192 Copynumber: 2.6 Consensus size: 191
16963702 ATCTTATACC
* * * * * * *
16963712 CTTAAAGCTGTAGAAGGGCAGATTGAAGCTGTAATGGCGAATCATATACCCCTAAAACTGTAGAG
1 CTTAAAGCTATAGAGGGGTAGATTGAAGCTGCAAAGGCGAATCTTATACCCCTAAAGCTGTA-AG
* * * * * * *
16963777 GGGCAAATTGAAGCTACAAAAGCGAATCTTATACCCTTAATA-TTGTAGAGGGGTAGATTAAAGC
65 GGGCAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAA-AGTTGTAAAGGGATAGATTAAAGC
* * * *
16963841 CACAAAGACGAATTTTATACCCCTAAAGCTATAGAGGGGCAGATTGAAGCTGCAAAGGTAAAT
129 CACAAAGACGAATCTTATACCACTAAAGCTATAGAGGGGCAAATTGAAGCCGCAAAGGTAAAT
* * **
16963904 CTTATAGCTATAGAGGGGTAGATTGAAGTTGCAAAGGCGAATCTTATGTCCCTAAAGCTGTAAAG
1 CTTAAAGCTATAGAGGGGTAGATTGAAGCTGCAAAGGCGAATCTTATACCCCTAAAGCTGT-AAG
* *
16963969 GGACAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGTTGTAAAGGGATAGATTGAAGCC
65 GGGCAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGTTGTAAAGGGATAGATTAAAGCC
* ** * * * * *
16964034 ACGAAGGTGAATCTTATACCAGTAAAGCTCTAGAGGGGTAAATTGAAGCCGCAAAGGTGATT
130 ACAAAGACGAATCTTATACCACTAAAGCTATAGAGGGGCAAATTGAAGCCGCAAAGGTAAAT
* * ** * *
16964096 CTTAAATCTCTA-AGGGGGTAGATTGAAGCCACGAAGGTGAATCTTATACCCCTAAAGCTG--AG
1 CTTAAAGCTATAGA-GGGGTAGATTGAAGCTGCAAAGGCGAATCTTATACCCCTAAAGCTGTAAG
* *
16964158 GGGCAGATTAAAGCCACGAAGGCAAATCTTATACCCCTAAAG
65 GGGCAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAG
16964200 CTATAGAAGG
Statistics
Matches: 248, Mismatches: 45, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
189 41 0.17
191 2 0.01
192 204 0.82
193 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (191 bp):
CTTAAAGCTATAGAGGGGTAGATTGAAGCTGCAAAGGCGAATCTTATACCCCTAAAGCTGTAAGG
GGCAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGTTGTAAAGGGATAGATTAAAGCCA
CAAAGACGAATCTTATACCACTAAAGCTATAGAGGGGCAAATTGAAGCCGCAAAGGTAAAT
Found at i:16964079 original size:50 final size:50
Alignment explanation
Indices: 16963909--16964252 Score: 235
Period size: 50 Copynumber: 7.1 Consensus size: 50
16963899 TAAATCTTAT
* * *** * * **
16963909 AGCTATAGAGGGGTAGATTGAAGTTGCAAAGGCGAATCTTATGTCCCTAA
1 AGCTCTAGAGGGGTAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAA
* * **
16963959 AGCTGTAAAGGGACAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAA
1 AGCTCTAGAGGGGTAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAA
* * * * * ** **
16964009 AGTTGTAAAGGGATAGATTGAAGCCACGAAGGTGAATCTTATACCAGTAA
1 AGCTCTAGAGGGGTAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAA
** * * *
16964059 AGCTCTAGAGGGGTAAATTGAAG-C-C----GCAAAGGTGAT--TCTTAA
1 AGCTCTAGAGGGGTAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAA
* * **
16964101 ATCTCTA-AGGGGGTAGATTGAAGCCACGAAGGTGAATCTTATACCCCTAA
1 AGCTCTAGA-GGGGTAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAA
* * *
16964151 AG--CT-GAGGGGCAGATTAAAGCCACGAAGGCAAATCTTATACCCCTAA
1 AGCTCTAGAGGGGTAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAA
* * * * *
16964198 AGCTATAGAAGGGCAAATTGAAGTCGCGAAGGCAAATCTTATACCCCCTAA
1 AGCTCTAGAGGGGTAAATTGAAGCCACGAAGGCAAATCTTATA-CCCCTAA
16964249 AGCT
1 AGCT
16964253 ATCAAGGGTT
Statistics
Matches: 228, Mismatches: 52, Indels: 27
0.74 0.17 0.09
Matches are distributed among these distances:
41 1 0.00
42 22 0.10
43 1 0.00
44 7 0.03
47 39 0.17
48 10 0.04
49 2 0.01
50 135 0.59
51 11 0.05
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (50 bp):
AGCTCTAGAGGGGTAAATTGAAGCCACGAAGGCAAATCTTATACCCCTAA
Found at i:16964178 original size:47 final size:48
Alignment explanation
Indices: 16964110--16964253 Score: 182
Period size: 47 Copynumber: 3.0 Consensus size: 48
16964100 AATCTCTAAG
* **
16964110 GGGGTAGATTGAAGCCACGAAGGTGAATCTTATACCCCTAAAGCT-GA
1 GGGGCAGATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGCTAGA
*
16964157 GGGGCAGATTAAAGCCACGAAGGCAAATCTTATACCCCTAAAGCTATAGA
1 GGGGCAGATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGC--TAGA
* * * *
16964207 AGGGCAAATTGAAGTCGCGAAGGCAAATCTTATACCCCCTAAAGCTA
1 GGGGCAGATTGAAGCCACGAAGGCAAATCTTATA-CCCCTAAAGCTA
16964254 TCAAGGGTTA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
47 40 0.48
49 3 0.04
50 31 0.37
51 10 0.12
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (48 bp):
GGGGCAGATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGCTAGA
Found at i:16964238 original size:139 final size:140
Alignment explanation
Indices: 16963975--16964238 Score: 341
Period size: 139 Copynumber: 1.9 Consensus size: 140
16963965 AAAGGGACAA
* * *
16963975 ATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGTTGTAAAGGGATAGATTGAAGCCACGAAG
1 ATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGCTG--AAGGGACAGATTAAAGCCACGAAG
** * * * * ** *
16964040 GTGAATCTTATACCAGTAAAGCTCTAGAGGGGTAAATTGAAGCCGCAAAGGTGATTCTTAAATCT
64 GCAAATCTTATACCACTAAAGCTATAGAAGGGCAAATTGAAGCCGCAAAGGCAAATCTTAAATCT
16964105 CTAAGGGGGTAG
129 CTAAGGGGGTAG
** *
16964117 ATTGAAGCCACGAAGGTGAATCTTATACCCCTAAAGCTG-AGGGGCAGATTAAAGCCACGAAGGC
1 ATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGCTGAAGGGACAGATTAAAGCCACGAAGGC
* * *
16964181 AAATCTTATACCCCTAAAGCTATAGAAGGGCAAATTGAAGTCGCGAAGGCAAATCTTA
66 AAATCTTATACCACTAAAGCTATAGAAGGGCAAATTGAAGCCGCAAAGGCAAATCTTA
16964239 TACCCCCTAA
Statistics
Matches: 104, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
139 68 0.65
142 36 0.35
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (140 bp):
ATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGCTGAAGGGACAGATTAAAGCCACGAAGGC
AAATCTTATACCACTAAAGCTATAGAAGGGCAAATTGAAGCCGCAAAGGCAAATCTTAAATCTCT
AAGGGGGTAG
Found at i:16964260 original size:50 final size:49
Alignment explanation
Indices: 16964117--16964304 Score: 186
Period size: 50 Copynumber: 3.8 Consensus size: 49
16964107 AAGGGGGTAG
** * *
16964117 ATTGAAGCCACGAAGGTGAATCTTATACCCCTAAAGC--TGAGGGGCAG
1 ATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGCTATGAAGGGCAA
*
16964164 ATTAAAGCCACGAAGGCAAATCTTATACCCCTAAAGCTATAGAAGGGCAA
1 ATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGCTAT-GAAGGGCAA
* * * * *
16964214 ATTGAAGTCGCGAAGGCAAATCTTATACCCCCTAAAGCTATCAAGGGTTAG
1 ATTGAAGCCACGAAGGCAAATCTTATA-CCCCTAAAGCTATGAAGGG-CAA
* * *
16964265 ATTGAAG-CA-GAAAAGACGAATCTTGTACCCCTAAAGCTAT
1 ATTGAAGCCACG--AAGGCAAATCTTATACCCCTAAAGCTAT
16964305 AGCCGCAAAG
Statistics
Matches: 119, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
47 34 0.29
49 2 0.02
50 50 0.42
51 33 0.28
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (49 bp):
ATTGAAGCCACGAAGGCAAATCTTATACCCCTAAAGCTATGAAGGGCAA
Found at i:16965481 original size:19 final size:19
Alignment explanation
Indices: 16965442--16965482 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
16965432 CGGGTTTATC
* *
16965442 TTTTAAAAAAATGATGTTT
1 TTTTAAAAAAATGAAGCTT
*
16965461 TTTTAAAAAAATTAAGCTT
1 TTTTAAAAAAATGAAGCTT
16965480 TTT
1 TTT
16965483 CTACCACCGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (19 bp):
TTTTAAAAAAATGAAGCTT
Found at i:16968363 original size:19 final size:18
Alignment explanation
Indices: 16968321--16968360 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
16968311 AAAAGTTATG
*
16968321 AAAATAAAACTAGAAACT
1 AAAATAAAAATAGAAACT
16968339 AAAATAAAAATAAGAAA-T
1 AAAATAAAAAT-AGAAACT
16968357 AAAA
1 AAAA
16968361 ATATTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAATAAAAATAGAAACT
Found at i:16979221 original size:12 final size:12
Alignment explanation
Indices: 16979206--16979230 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16979196 CGACCATGCC
16979206 CCAGACCGTGTG
1 CCAGACCGTGTG
16979218 CCAGACCGTGTG
1 CCAGACCGTGTG
16979230 C
1 C
16979231 ATACATGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (12 bp):
CCAGACCGTGTG
Found at i:16979282 original size:12 final size:12
Alignment explanation
Indices: 16979267--16979297 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16979257 TGTCACAGAT
16979267 CGTGTGACAAAC
1 CGTGTGACAAAC
*
16979279 CGTGTGACAAGC
1 CGTGTGACAAAC
16979291 CGTGTGA
1 CGTGTGA
16979298 ACATGCGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.32, T:0.19
Consensus pattern (12 bp):
CGTGTGACAAAC
Found at i:16986030 original size:28 final size:26
Alignment explanation
Indices: 16985967--16986022 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
16985957 TCATTGTTAC
16985967 ATCAC-AA-AATGAATCAATATTCAT
1 ATCACAAATAATGAATCAATATTCAT
*
16985991 ATCACAAATAATGACATCTATATTCCAT
1 ATCACAAATAATGA-ATCAATATT-CAT
16986019 ATCA
1 ATCA
16986023 ACCATAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 5 0.19
25 2 0.07
26 5 0.19
27 8 0.30
28 7 0.26
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (26 bp):
ATCACAAATAATGAATCAATATTCAT
Found at i:16987216 original size:36 final size:36
Alignment explanation
Indices: 16987175--16987265 Score: 173
Period size: 36 Copynumber: 2.5 Consensus size: 36
16987165 TGATTACTCT
16987175 TGTTGACCCAAAGGTCATGATGCTCATTTTACTCCC
1 TGTTGACCCAAAGGTCATGATGCTCATTTTACTCCC
16987211 TGTTGACCCAAAGGTCATGATGCTCATTTTACTCCC
1 TGTTGACCCAAAGGTCATGATGCTCATTTTACTCCC
*
16987247 TATTGACCCAAAGGTCATG
1 TGTTGACCCAAAGGTCATG
16987266 CCTGTTACCA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (36 bp):
TGTTGACCCAAAGGTCATGATGCTCATTTTACTCCC
Found at i:16999889 original size:32 final size:32
Alignment explanation
Indices: 16999851--16999927 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
16999841 ACGCGAACCC
* *
16999851 TGTATGTGATGTTTGAACCTATGCTGTGTGAT
1 TGTATGTGATGTGTGAACCTATGCTATGTGAT
*
16999883 TGTATGTGATGTGTGAACCTATGCTATGTGAC
1 TGTATGTGATGTGTGAACCTATGCTATGTGAT
* *
16999915 TATGTGTGATGTG
1 TGTATGTGATGTG
16999928 CGATCTTATG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.19, C:0.09, G:0.30, T:0.42
Consensus pattern (32 bp):
TGTATGTGATGTGTGAACCTATGCTATGTGAT
Found at i:16999952 original size:23 final size:22
Alignment explanation
Indices: 16999920--16999999 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
16999910 GTGACTATGT
* *
16999920 GTGATGTGCGATCTTATGCTAAA
1 GTGATATGCGAAC-TATGCTAAA
*
16999943 GTGATATGCGAAC-ATGCTATA
1 GTGATATGCGAACTATGCTAAA
* *
16999964 -TGTTATGTGAACTGATGCTAAA
1 GTGATATGCGAACT-ATGCTAAA
16999986 GTGATATGCGAACT
1 GTGATATGCGAACT
17000000 TCTAATATGA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 10 0.22
21 7 0.15
22 7 0.15
23 22 0.48
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (22 bp):
GTGATATGCGAACTATGCTAAA
Found at i:17010324 original size:52 final size:52
Alignment explanation
Indices: 17010169--17010357 Score: 270
Period size: 52 Copynumber: 3.6 Consensus size: 52
17010159 GCCATAAACG
* *
17010169 AAAAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACAGATT
1 AAAAGGTCCAATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* *
17010221 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
1 AAAAGGTCCAATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* **
17010273 AAAAGGTCCAATGACTAAGTGTCATCGTGAGTATATGAATCCCTTGTGGATT
1 AAAAGGTCCAATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * * * *
17010325 ATAAGGTCCAGTGGCTATGTGTCATTGTGAGTA
1 AAAAGGTCCAATGACTAAGTGTCATCGTGAGTA
17010358 AAGGAAAGAA
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (52 bp):
AAAAGGTCCAATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
Found at i:17012173 original size:23 final size:24
Alignment explanation
Indices: 17012134--17012181 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
17012124 TTTATTTGAT
17012134 AATGTGTTTTGATATAACAAATTAA
1 AATGTGTTTTGATATAA-AAATTAA
*
17012159 AATGT-TTTTGA-ATAAAAGTTAA
1 AATGTGTTTTGATATAAAAATTAA
17012181 A
1 A
17012182 GTTGAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 6 0.27
25 5 0.23
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (24 bp):
AATGTGTTTTGATATAAAAATTAA
Found at i:17013412 original size:16 final size:17
Alignment explanation
Indices: 17013381--17013413 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17013371 GTTCTCCTAA
17013381 AAATAACAATTTTAATT
1 AAATAACAATTTTAATT
*
17013398 AAATTACAA-TTTAATT
1 AAATAACAATTTTAATT
17013414 TCGCCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATAACAATTTTAATT
Found at i:17016956 original size:163 final size:157
Alignment explanation
Indices: 17016626--17017291 Score: 559
Period size: 163 Copynumber: 4.2 Consensus size: 157
17016616 CATCATACAG
* ** *
17016626 TTCCATTACTAAAGACTTGAGTTGCAAAAAAGGATGCCGGGTACTTTCAACAACAATAAAACCTA
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATGCAAGGTACTTTTAACAACAATAAAACCTA
* * **
17016691 TATGCT-T--TT-GTTCTATATTA-TCCAGACTCTTCATTTTCCTAAAGAATCCATGTC--ACAT
66 TATGCTCTGCTTAATTTTATATTACT-CAGACTCTTCATTTTTGTAAAGAATCCATGTCTAACAT
* * **
17016749 ATTCAAACATGGAAAAGGAAGTACAATC
130 ATTCAAACATGGATACGGAAGTATGATC
** * * *
17016777 TTCCATTTCTAAAGACTCGAGCTGCAAAAAAGGATGCAAGGTACTTTTAACAGCAATAAAACCTA
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATGCAAGGTACTTTTAACAACAATAAAACCTA
*
17016842 TATGCTCATGCTTAATTTTATGTTACTCAGACTCATTCATATTTTGTAAAAGAATCCATGTCTAA
66 TATGCTC-TGCTTAATTTTATATTACTCAGACTC-TTCAT-TTTTGT-AAAGAATCCATGTCT-A
* * *
17016907 TACATATTCAGACATGGATACGAAAGCATGATC
126 -ACATATTCAAACATGGATACGGAAGTATGATC
* * * *
17016940 TTCCATCACTAAAGACTTGAGCTGCAAAAAAGGATGCAGGGTACTTTTAACAACAATGAAACATA
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATGCAAGGTACTTTTAACAACAATAAAACCTA
* * * ** *** *
17017005 GATGCTTCTGCTTAACTCTTA-ATTACCCCTACTCTTCATTTTCT-TAAAGAATTTGTGTTTTAA
66 TATGC-TCTGCTTAA-TTTTATATTACTCAGACTCTTCATTTT-TGTAAAGAATCCATG-TCT-A
** *
17017068 CACATATTCAGGCATGGATACGGAGGTATGATC
126 -ACATATTCAAACATGGATACGGAAGTATGATC
* * * * * * *
17017101 TTCCATCATTACATACTTGAGTTGCAAAAAAGGACGCAAGGCACTTTTAACAGCAAT-AAAGCT-
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATGCAAGGTACTTTTAACAACAATAAAACCTA
* * * * ** *
17017164 TA--CTCATGCTTAACTTCATGTTACCGCCCACTCTTCATTTTTTGTAAAAGAATCCATATCTAA
66 TATGCTC-TGCTTAATTTTATATTA-CTCAGACTCTTCA-TTTTTGT-AAAGAATCCATGTCTAA
* * **
17017227 CACATTCAAAAATGGATGTGG-AGATATGATC
127 CATATTCAAACATGGATACGGAAG-TATGATC
* *
17017258 TTCCATCACTAAAGGCTTGAGTTGCAAGAAAGGA
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGA
17017292 CATAAGGACA
Statistics
Matches: 416, Mismatches: 75, Indels: 42
0.78 0.14 0.08
Matches are distributed among these distances:
151 64 0.15
153 1 0.00
155 2 0.00
156 20 0.05
157 69 0.17
158 17 0.04
159 22 0.05
160 21 0.05
161 85 0.20
162 6 0.01
163 103 0.25
164 6 0.01
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.31
Consensus pattern (157 bp):
TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATGCAAGGTACTTTTAACAACAATAAAACCTA
TATGCTCTGCTTAATTTTATATTACTCAGACTCTTCATTTTTGTAAAGAATCCATGTCTAACATA
TTCAAACATGGATACGGAAGTATGATC
Found at i:17018983 original size:8 final size:9
Alignment explanation
Indices: 17018961--17019011 Score: 59
Period size: 10 Copynumber: 5.6 Consensus size: 9
17018951 TAAGTTATAG
17018961 AAAATTAAT
1 AAAATTAAT
17018970 AAAATTAA-
1 AAAATTAAT
*
17018978 AAAATTATT
1 AAAATTAAT
17018987 AACAATTAAT
1 AA-AATTAAT
*
17018997 AAAAGTTTAT
1 AAAA-TTAAT
17019007 AAAAT
1 AAAAT
17019012 AAAAATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 7 0.19
9 13 0.36
10 16 0.44
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAATTAAT
Found at i:17019414 original size:11 final size:10
Alignment explanation
Indices: 17019370--17019443 Score: 55
Period size: 10 Copynumber: 7.2 Consensus size: 10
17019360 AATTTTTTGC
17019370 ATAATTTTTA
1 ATAATTTTTA
*
17019380 ATAATTTTAA
1 ATAATTTTTA
17019390 ATACATTTTATA
1 ATA-ATTTT-TA
17019402 ATAA--TTTA
1 ATAATTTTTA
* *
17019410 TTAATTTCTA
1 ATAATTTTTA
17019420 ATAATCTTTT-
1 ATAAT-TTTTA
17019430 ATGAATTTTATA
1 AT-AATTTT-TA
17019442 AT
1 AT
17019444 TTATGATTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
8 5 0.10
9 2 0.04
10 24 0.48
11 13 0.26
12 6 0.12
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:17019448 original size:16 final size:16
Alignment explanation
Indices: 17019427--17019477 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
17019417 CTAATAATCT
17019427 TTTATGAATTTTATAA
1 TTTATGAATTTTATAA
* *
17019443 TTTATG-ATTTAAAAA
1 TTTATGAATTTTATAA
17019458 TATTAT-AATTTTAATAA
1 T-TTATGAATTTT-ATAA
17019475 TTT
1 TTT
17019478 TTACTTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 8 0.29
16 16 0.57
17 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
TTTATGAATTTTATAA
Found at i:17037140 original size:21 final size:21
Alignment explanation
Indices: 17037116--17037156 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17037106 CAATCAACTA
*
17037116 TCAACTGTCAAAGGTCAACGG
1 TCAACCGTCAAAGGTCAACGG
*
17037137 TCAACCGTCAATGGTCAACG
1 TCAACCGTCAAAGGTCAACG
17037157 ATTTGGGTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.20
Consensus pattern (21 bp):
TCAACCGTCAAAGGTCAACGG
Found at i:17049464 original size:26 final size:26
Alignment explanation
Indices: 17049435--17049623 Score: 143
Period size: 26 Copynumber: 7.4 Consensus size: 26
17049425 CTTATCAAAA
* * *
17049435 TATTTATGCGTTTATGCTTGTCAGCT
1 TATTTATGCGTTTACGCTCGCCAGCT
*
17049461 TATTTATGTGTTTACGCTCGCCAGC-
1 TATTTATGCGTTTACGCTCGCCAGCT
** ** * * * **
17049486 T-TGCACACTTTTATGCTTGTTAGCT
1 TATTTATGCGTTTACGCTCGCCAGCT
* *
17049511 TATTTATGTGTTTACGCTCTCCAGCT
1 TATTTATGCGTTTACGCTCGCCAGCT
* *
17049537 TATTTATACGTTTACACTCGCCAG-T
1 TATTTATGCGTTTACGCTCGCCAGCT
** ** *
17049562 T-TGCACACGTTTACGCTCGTCAGCT
1 TATTTATGCGTTTACGCTCGCCAGCT
*
17049587 TATTTATGCGTTTACACTCGCCAGCT
1 TATTTATGCGTTTACGCTCGCCAGCT
17049613 TATTTATGCGT
1 TATTTATGCGT
17049624 ATATATATAA
Statistics
Matches: 119, Mismatches: 40, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
24 30 0.25
25 6 0.05
26 83 0.70
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (26 bp):
TATTTATGCGTTTACGCTCGCCAGCT
Found at i:17049566 original size:76 final size:76
Alignment explanation
Indices: 17049435--17049619 Score: 235
Period size: 76 Copynumber: 2.4 Consensus size: 76
17049425 CTTATCAAAA
** * * ** * * *
17049435 TATTTATGCGTTTATGCTTGTCAGCTTATTTATGTGTTTACGCTCGCCAGCTTGCACACTTTTAT
1 TATTTATGCGTTTACACTCGCCAGCTTATTTATACGTTTACACTCGCCAGCTTGCACACGTTTAC
* *
17049500 GCTTGTTAGCT
66 GCTCGTCAGCT
* * * *
17049511 TATTTATGTGTTTACGCTCTCCAGCTTATTTATACGTTTACACTCGCCAGTTTGCACACGTTTAC
1 TATTTATGCGTTTACACTCGCCAGCTTATTTATACGTTTACACTCGCCAGCTTGCACACGTTTAC
17049576 GCTCGTCAGCT
66 GCTCGTCAGCT
17049587 TATTTATGCGTTTACACTCGCCAGCTTATTTAT
1 TATTTATGCGTTTACACTCGCCAGCTTATTTAT
17049620 GCGTATATAT
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
76 93 1.00
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.43
Consensus pattern (76 bp):
TATTTATGCGTTTACACTCGCCAGCTTATTTATACGTTTACACTCGCCAGCTTGCACACGTTTAC
GCTCGTCAGCT
Found at i:17079213 original size:36 final size:36
Alignment explanation
Indices: 17079166--17079267 Score: 125
Period size: 36 Copynumber: 2.8 Consensus size: 36
17079156 TTCGATGGAA
* *
17079166 TGCTTACGTCTCGGTTAGAGCTTAATGCTAAGAGCT
1 TGCTTACGTCTCGATTAGAGCTTAATGCTAAGAGAT
* * * *
17079202 TGCTTACGTCTCTATTAGAGCATAATGCTATGTGAT
1 TGCTTACGTCTCGATTAGAGCTTAATGCTAAGAGAT
*
17079238 TGATTACGTCTCGATTAGAG-TGTAATGCTA
1 TGCTTACGTCTCGATTAGAGCT-TAATGCTA
17079268 TGTCTCGGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (36 bp):
TGCTTACGTCTCGATTAGAGCTTAATGCTAAGAGAT
Found at i:17079279 original size:24 final size:24
Alignment explanation
Indices: 17079245--17079291 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
17079235 GATTGATTAC
**
17079245 GTCTCGATTAGAGTGTAATGCTAT
1 GTCTCGATTAGAGCATAATGCTAT
*
17079269 GTCTCGGTTAGAGCATAATGCTA
1 GTCTCGATTAGAGCATAATGCTA
17079292 AGTGATTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (24 bp):
GTCTCGATTAGAGCATAATGCTAT
Found at i:17082667 original size:20 final size:21
Alignment explanation
Indices: 17082630--17082685 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
17082620 ATCAGTAAGC
*
17082630 CTTAATT-AATCATTTTTA-A
1 CTTAATTAAATCATATTTACA
17082649 TCTTAATTAAATC-TATTTACA
1 -CTTAATTAAATCATATTTACA
*
17082670 CTTAATATAAACCATA
1 CTTAAT-TAAATCATA
17082686 CTAATCCACT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 18 0.60
21 10 0.33
22 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (21 bp):
CTTAATTAAATCATATTTACA
Found at i:17088135 original size:21 final size:21
Alignment explanation
Indices: 17088110--17088187 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
17088100 CCTTCAACTT
*
17088110 CTACCGATACAAGCACACCAA
1 CTACCGATACAAGTACACCAA
*
17088131 CTACCGATACATTAGTACACAAAA
1 CTACCGATACA--AGTACAC-CAA
* *
17088155 CTACCGATACTAGTA-ATTCAA
1 CTACCGATACAAGTACA-CCAA
17088176 CTACCGATACAA
1 CTACCGATACAA
17088188 CTTAAGTCAG
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
21 25 0.53
22 4 0.09
23 6 0.13
24 12 0.26
ACGTcount: A:0.42, C:0.29, G:0.09, T:0.19
Consensus pattern (21 bp):
CTACCGATACAAGTACACCAA
Found at i:17089881 original size:20 final size:20
Alignment explanation
Indices: 17089843--17089881 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
17089833 CATCATTATG
*
17089843 TCTTAATTAATAATTTTTAA
1 TCTTAATTAATAATATTTAA
17089863 TCTTAATTAA-ATATATTTA
1 TCTTAATTAATA-ATATTTA
17089882 CACTTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
TCTTAATTAATAATATTTAA
Found at i:17101042 original size:21 final size:21
Alignment explanation
Indices: 17101018--17101067 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
17101008 TGAGACAATA
17101018 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* *
17101039 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
17101060 CTACCGAT
1 CTACCGAT
17101068 GCTAAAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:17117353 original size:23 final size:24
Alignment explanation
Indices: 17117326--17117405 Score: 117
Period size: 26 Copynumber: 3.3 Consensus size: 24
17117316 AACTCTATCT
17117326 GGCTCGTAAGAGCTAACCATTCT-
1 GGCTCGTAAGAGCTAACCATTCTG
* *
17117349 GGCTCGTAAGAGTTAACCATTATG
1 GGCTCGTAAGAGCTAACCATTCTG
17117373 GGCTCGTGTAAGAGCTAACCATTCTG
1 GGCTC--GTAAGAGCTAACCATTCTG
17117399 GGCTCGT
1 GGCTCGT
17117406 GTGGGCTAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
23 21 0.42
24 7 0.14
26 22 0.44
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAACCATTCTG
Found at i:17119128 original size:29 final size:29
Alignment explanation
Indices: 17119086--17119148 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
17119076 TAACACATTT
* *
17119086 CAAGATGTGATAGATCCTGCTGACAATTC
1 CAAGATGTGATAGATCCTGCCGACAATCC
* *
17119115 CAAGATGTGATAGATCTTGCCGGCAATCC
1 CAAGATGTGATAGATCCTGCCGACAATCC
17119144 CAAGA
1 CAAGA
17119149 ACCATGTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (29 bp):
CAAGATGTGATAGATCCTGCCGACAATCC
Found at i:17123803 original size:20 final size:22
Alignment explanation
Indices: 17123765--17123816 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
17123755 CATCATTATG
*
17123765 TCTTAATT-AATAATTTTTA-A
1 TCTTAATTAAATAATATTTACA
17123785 TCTTAATTAAAT-ATATTTACA
1 TCTTAATTAAATAATATTTACA
17123806 -CTTAATATAAA
1 TCTTAAT-TAAA
17123817 CCATACTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (22 bp):
TCTTAATTAAATAATATTTACA
Found at i:17135035 original size:21 final size:21
Alignment explanation
Indices: 17135011--17135060 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
17135001 TGAGACAATA
17135011 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* *
17135032 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
17135053 CTACCGAT
1 CTACCGAT
17135061 GCTAAAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:17141477 original size:200 final size:194
Alignment explanation
Indices: 17141028--17141477 Score: 460
Period size: 195 Copynumber: 2.3 Consensus size: 194
17141018 ACCATACTCG
* * * ** * * *
17141028 ATGCTGCTCACACGAGTTGTCGAGGATTCGTAACGTATGTAGTACCCCAGCCATCGGTACGGTGC
1 ATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACGGTAC
* * * *
17141093 CTGTCTGTACTATAAACTATTCCCTAACGATGCTCCTCACACGAGCTGTCGAGAGTGTACAATAA
66 CTG-CTGCACTATAAACTATTCCCTAACGATGCTCCTCACACGAGCTATCGAGAATATACAATAA
* * * *
17141158 GCACAGTCCCAGCCATAGTAGGGCATGTAATCCATTTAGGATCCATATATCTTTCCCGAGTCACA
130 GCAAAATCCCAACCATAGTAGGGCATGTAATCCATTTAGGATCCATATATCTTTCCCGACTCACA
* * * * * * *
17141223 ATGCTGGTCACACAAGCTATCGAGGACTCGCAACATATGCGGTACTTGAGCCATCGATACGGTAT
1 ATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACGGTAC
* * * *
17141288 CTG-TGCA-TAT-AACTGTTCCCTAACGATGCTGCTCACACGAGCTATCG-GTAATATGCACTTA
66 CTGCTGCACTATAAACTATTCCCTAACGATGCTCCTCACACGAGCTATCGAG-AATATACA-ATA
* * * *
17141349 TGCATAAATCTCAACCATCGTAGGGCATGTAATCCATTTAGGATCCATATTTCTTTTCTCATTTC
129 AGCA-AAATCCCAACCATAGTAGGGCATGTAATCCATTTAGGATCCATATATC--TT-TC----C
17141414 CTGACTCACA
186 C-GACTCACA
* *
17141424 ATTCTGCT-TCACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATC
1 ATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATC
17141478 ACATCAAATT
Statistics
Matches: 205, Mismatches: 39, Indels: 17
0.79 0.15 0.07
Matches are distributed among these distances:
190 1 0.00
191 39 0.19
192 8 0.04
193 45 0.22
195 55 0.27
196 2 0.01
200 42 0.20
201 13 0.06
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (194 bp):
ATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACGGTAC
CTGCTGCACTATAAACTATTCCCTAACGATGCTCCTCACACGAGCTATCGAGAATATACAATAAG
CAAAATCCCAACCATAGTAGGGCATGTAATCCATTTAGGATCCATATATCTTTCCCGACTCACA
Found at i:17156767 original size:378 final size:379
Alignment explanation
Indices: 17156069--17156829 Score: 1254
Period size: 378 Copynumber: 2.0 Consensus size: 379
17156059 TGGTTATTAT
* **
17156069 AAAAATGGGTGCCTTGGTCACTTATCAACACTCTCGGTGTTTCAAATCTCGTGAGGATGTATGTG
1 AAAAATGGGTGCCTTGGTCACTTATCAACACTCTCGGTGTTCCAAATCTCGTGAGGATGTATGCA
*
17156134 TGAAAGAACTTCAATACCGTTTGAGCATCATCTTTTGGCATCGCAATAGCCTCGATCCACTTCGA
66 TGAAAGAACTTCAATACCGTCTGAGCATCATCTTTTGGCATCGCAATAGCCTCGATCCACTTCGA
* * *
17156199 GACATAGTCAACAACCACTAAAATATACACATTTTCAAAAGAGTTTGGAAATGGTCTCATAAAGT
131 GACATAGTCAACAACCACCAAAATATACACATTTCCAAAAAAGTTTGGAAATGGTCTCATAAAGT
*
17156264 CTATACCCCAAACATCAAAGAGCTTTACCTCTATCATGGGTTGTTAGAGCATCTCAATGCGTCGA
196 CTATACCCCAAACATCAAAGAGCTCTACCTCTATCATGGGTTGTTAGAGCATCTCAATGCGTCGA
* *
17156329 GATATTAAACCAATGTGTTGACAACGATCACATTGTTGTGCGAAGTTGTGAGCATCTCGAAACAA
261 GATATTAAACCAATGCGTTGACAACGATCACATTGTTGTGCAAAGTTGTGAGCATCTCGAAACAA
17156394 TGT-GGCAAATAAAATCCTGACTGTAAAACCTTCGCAACAGTCCTTGTTCCACC
326 TGTGGGCAAATAAAATCCTGACTGTAAAACCTTCGCAACAGTCCTTGTTCCACC
*
17156447 AAAAATGGGTGCCTTGGTCACTTATCAACGCTCTCGGTGTTCCAAATCTCGTGAGGATGTATGCA
1 AAAAATGGGTGCCTTGGTCACTTATCAACACTCTCGGTGTTCCAAATCTCGTGAGGATGTATGCA
* *
17156512 TGAAAGAACTTTAATACCGTCTGAGCATCATCTTTTGGCATCGCAATAGCCTTGATCCACTTCGA
66 TGAAAGAACTTCAATACCGTCTGAGCATCATCTTTTGGCATCGCAATAGCCTCGATCCACTTCGA
* * *
17156577 GACGTAGTCAACAGCCACCAAAATATACGCATTTCCAAAAAAGTTTGGAAATGGTCTCATAAAGT
131 GACATAGTCAACAACCACCAAAATATACACATTTCCAAAAAAGTTTGGAAATGGTCTCATAAAGT
* * * * *
17156642 CTATACCCTAAACTTCAAAGAGCTCTACCTCTATGATGGGTTGTTGGAGCATCTCATTGCGTCGA
196 CTATACCCCAAACATCAAAGAGCTCTACCTCTATCATGGGTTGTTAGAGCATCTCAATGCGTCGA
* * *
17156707 GATATTGAACCAGTGCGTTGACAACGATCACATTGTTGTGCAAAGTTGTGAGCGTCTCGAAACAA
261 GATATTAAACCAATGCGTTGACAACGATCACATTGTTGTGCAAAGTTGTGAGCATCTCGAAACAA
* * * **
17156772 TGTGGGCCAATAAAATCTTGACTGTAAAACCTTTGCAGTAGTCCTTGTTCCACC
326 TGTGGGCAAATAAAATCCTGACTGTAAAACCTTCGCAACAGTCCTTGTTCCACC
17156826 AAAA
1 AAAA
17156830 TGGCCTTCAT
Statistics
Matches: 353, Mismatches: 29, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
378 304 0.86
379 49 0.14
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (379 bp):
AAAAATGGGTGCCTTGGTCACTTATCAACACTCTCGGTGTTCCAAATCTCGTGAGGATGTATGCA
TGAAAGAACTTCAATACCGTCTGAGCATCATCTTTTGGCATCGCAATAGCCTCGATCCACTTCGA
GACATAGTCAACAACCACCAAAATATACACATTTCCAAAAAAGTTTGGAAATGGTCTCATAAAGT
CTATACCCCAAACATCAAAGAGCTCTACCTCTATCATGGGTTGTTAGAGCATCTCAATGCGTCGA
GATATTAAACCAATGCGTTGACAACGATCACATTGTTGTGCAAAGTTGTGAGCATCTCGAAACAA
TGTGGGCAAATAAAATCCTGACTGTAAAACCTTCGCAACAGTCCTTGTTCCACC
Found at i:17161414 original size:26 final size:26
Alignment explanation
Indices: 17161384--17161436 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
17161374 CTCTATCTGG
17161384 CTCGTAAGAGCTAACCATTCTGGGCT
1 CTCGTAAGAGCTAACCATTCTGGGCT
17161410 CTCGTAAGAGCTAACCATTCTGGGCT
1 CTCGTAAGAGCTAACCATTCTGGGCT
17161436 C
1 C
17161437 GTGTGGGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (26 bp):
CTCGTAAGAGCTAACCATTCTGGGCT
Found at i:17163165 original size:29 final size:29
Alignment explanation
Indices: 17163123--17163185 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
17163113 TAACACATTT
* *
17163123 CAAGATGTGATAGATCCTGCTGACAATTC
1 CAAGATGTGATAGATCCTGCCGACAATCC
* *
17163152 CAAGATGTGATAGATCTTGCCGGCAATCC
1 CAAGATGTGATAGATCCTGCCGACAATCC
17163181 CAAGA
1 CAAGA
17163186 ACCATGTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (29 bp):
CAAGATGTGATAGATCCTGCCGACAATCC
Found at i:17166368 original size:114 final size:114
Alignment explanation
Indices: 17166134--17166351 Score: 355
Period size: 114 Copynumber: 1.9 Consensus size: 114
17166124 TGCTCAGCGG
*
17166134 GAGATTGCAGTATATGAAATTTGTGGTAAGCACGATTTGGCCTGAGGACGAGGCAATCAGTAAGG
1 GAGATTGCAGTATATGAAATTTGTGGTAAGCACGATTTGGCCTGAGGACAAGGCAATCAGTAAGG
** * **
17166199 GTATTTCTTGGGCTTGCTCTACAAATATGTCAGGGTTTGTGCTCGGAGG
66 GTATTTCTTGGGCTTGCTCTACAAATATGTCAAAGTTTGTGATCGGAAA
*
17166248 GAGATTGCAGTATATGGAATTTGTGGTAAGCACGATTTGGCCTGAGGACAAGGCAAATCAGTAAG
1 GAGATTGCAGTATATGAAATTTGTGGTAAGCACGATTTGGCCTGAGGACAAGGC-AATCAGTAAG
17166313 GGTATTTCTTGGGCTTGCTCTACAAATATGTCCAAAGTT
65 GGTATTTCTTGGGCTTGCTCTACAAATATGT-CAAAGTT
17166352 ATTATTGAAA
Statistics
Matches: 98, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
114 52 0.53
115 41 0.42
116 5 0.05
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (114 bp):
GAGATTGCAGTATATGAAATTTGTGGTAAGCACGATTTGGCCTGAGGACAAGGCAATCAGTAAGG
GTATTTCTTGGGCTTGCTCTACAAATATGTCAAAGTTTGTGATCGGAAA
Found at i:17170461 original size:30 final size:30
Alignment explanation
Indices: 17170427--17170483 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17170417 TTTGTTTCAG
*
17170427 GTTCT-ATATTATTATTATCTTCTAATACTT
1 GTTCTAAT-TTATTATTAACTTCTAATACTT
*
17170457 GTTCTAATTTTTTATTAACTTCTAATA
1 GTTCTAATTTATTATTAACTTCTAATA
17170484 GCATACCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (30 bp):
GTTCTAATTTATTATTAACTTCTAATACTT
Found at i:17173589 original size:26 final size:28
Alignment explanation
Indices: 17173533--17173592 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
17173523 TTGCAGCCCC
* *
17173533 TTAAAAGTTGATAATTTTTTTTTGACAT
1 TTAAAAGTTGATAAATTTTTTTGGACAT
*
17173561 TTAAAAGTT-A-AAATTTTTTTGGACCT
1 TTAAAAGTTGATAAATTTTTTTGGACAT
17173587 TTAAAA
1 TTAAAA
17173593 ACTAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 19 0.66
27 1 0.03
28 9 0.31
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (28 bp):
TTAAAAGTTGATAAATTTTTTTGGACAT
Found at i:17173598 original size:26 final size:26
Alignment explanation
Indices: 17173548--17173599 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
17173538 AGTTGATAAT
* **
17173548 TTTTTTTTGACATTTAAAAGTTAAAA
1 TTTTTTTGGACATTTAAAAACTAAAA
*
17173574 TTTTTTTGGACCTTTAAAAACTAAAA
1 TTTTTTTGGACATTTAAAAACTAAAA
17173600 AAAATATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (26 bp):
TTTTTTTGGACATTTAAAAACTAAAA
Found at i:17184249 original size:16 final size:16
Alignment explanation
Indices: 17184228--17184262 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
17184218 ATACGTGAAG
17184228 AGATTTAAAAATTCAT
1 AGATTTAAAAATTCAT
17184244 AGATTTAAAAATTCAT
1 AGATTTAAAAATTCAT
17184260 AGA
1 AGA
17184263 ATTATGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (16 bp):
AGATTTAAAAATTCAT
Found at i:17186179 original size:17 final size:17
Alignment explanation
Indices: 17186159--17186196 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
17186149 AAAGTAGTTA
* *
17186159 AAAGAATATGAAAGGTT
1 AAAGAAGATGAAAGATT
17186176 AAAGAAGATGAAAGATT
1 AAAGAAGATGAAAGATT
17186193 AAAG
1 AAAG
17186197 GTCAAGGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (17 bp):
AAAGAAGATGAAAGATT
Found at i:17186431 original size:16 final size:16
Alignment explanation
Indices: 17186410--17186445 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
17186400 ATGGAATAGA
*
17186410 GTAATATAATAGAACT
1 GTAATAGAATAGAACT
17186426 GTAATAGAATAGAACT
1 GTAATAGAATAGAACT
17186442 GTAA
1 GTAA
17186446 CAAGTAATTC
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:0.50, C:0.06, G:0.17, T:0.28
Consensus pattern (16 bp):
GTAATAGAATAGAACT
Found at i:17188925 original size:20 final size:20
Alignment explanation
Indices: 17188900--17188946 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
17188890 CTTGTAGAGG
* * *
17188900 TTTGCACTTTTGTGTCCCTA
1 TTTGCACTCTAGTGCCCCTA
17188920 TTTGCACTCTAGTGCCCCTA
1 TTTGCACTCTAGTGCCCCTA
*
17188940 ATTGCAC
1 TTTGCAC
17188947 AATCATTCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.30, G:0.15, T:0.40
Consensus pattern (20 bp):
TTTGCACTCTAGTGCCCCTA
Found at i:17190314 original size:37 final size:38
Alignment explanation
Indices: 17190240--17190321 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 38
17190230 ACAAGTTGTT
17190240 TTAAAATTATTAAAATAATTTTTTGAAATATAAAATTA
1 TTAAAATTATTAAAATAATTTTTTGAAATATAAAATTA
* * *
17190278 TTAAAATTATT-ATATTATTATTTT-CAATATAAAATTA
1 TTAAAATTATTAAAATAATT-TTTTGAAATATAAAATTA
17190315 TTAAAAT
1 TTAAAAT
17190322 AGAACGTTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 25 0.62
38 15 0.38
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (38 bp):
TTAAAATTATTAAAATAATTTTTTGAAATATAAAATTA
Found at i:17190826 original size:15 final size:15
Alignment explanation
Indices: 17190778--17190826 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
17190768 TGGGTAAGGG
17190778 TTTTGA-TTTGGAGA
1 TTTTGATTTTGGAGA
* *
17190792 TTTTTG-TTTAGG-GT
1 -TTTTGATTTTGGAGA
17190806 TTTTGATTTTGGAGA
1 TTTTGATTTTGGAGA
17190821 TTTTGA
1 TTTTGA
17190827 GGATTGCTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 5 0.19
14 6 0.22
15 16 0.59
ACGTcount: A:0.16, C:0.00, G:0.27, T:0.57
Consensus pattern (15 bp):
TTTTGATTTTGGAGA
Found at i:17191452 original size:24 final size:23
Alignment explanation
Indices: 17191425--17191483 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 23
17191415 AAACTTTAAA
*
17191425 AATAGATTTTAATATAATAATTTT
1 AATA-ATTTTAATAAAATAATTTT
17191449 AATAATTTTATATAAAATAATTTT
1 AATAATTTTA-ATAAAATAATTTT
17191473 AATAATTTTAA
1 AATAATTTTAA
17191484 AATCATTTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 7 0.21
24 26 0.79
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
AATAATTTTAATAAAATAATTTT
Found at i:17191453 original size:9 final size:9
Alignment explanation
Indices: 17191439--17191483 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
17191429 GATTTTAATA
17191439 TAATAATTT
1 TAATAATTT
17191448 TAATAATTT
1 TAATAATTT
17191457 TATATAA---
1 TA-ATAATTT
17191464 -AATAATTT
1 TAATAATTT
17191472 TAATAATTT
1 TAATAATTT
17191481 TAA
1 TAA
17191484 AATCATTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
5 4 0.13
6 1 0.03
9 22 0.71
10 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TAATAATTT
Found at i:17192272 original size:20 final size:20
Alignment explanation
Indices: 17192247--17192285 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
17192237 GTGGTGATAC
17192247 GGTGGTGCTAG-GGTGGTGGG
1 GGTGGTGC-AGTGGTGGTGGG
*
17192267 GGTGGTTCAGTGGTGGTGG
1 GGTGGTGCAGTGGTGGTGG
17192286 TATGGTGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.05, C:0.05, G:0.62, T:0.28
Consensus pattern (20 bp):
GGTGGTGCAGTGGTGGTGGG
Found at i:17193133 original size:23 final size:23
Alignment explanation
Indices: 17193116--17193285 Score: 268
Period size: 23 Copynumber: 7.4 Consensus size: 23
17193106 TAATCATAGA
*
17193116 AATATTTAAGCATAAATCATATT
1 AATATTTAAGCATAAATCACATT
*
17193139 AATATTTAAGCACAAATCACATT
1 AATATTTAAGCATAAATCACATT
17193162 AATATTTAAGCATAAATCACATT
1 AATATTTAAGCATAAATCACATT
*
17193185 AATATTTAAGCACAAATCACATT
1 AATATTTAAGCATAAATCACATT
17193208 AATATTTAAGCATAAATCACATT
1 AATATTTAAGCATAAATCACATT
* * *
17193231 AATATTTAGGTATAAACCACATT
1 AATATTTAAGCATAAATCACATT
* *
17193254 AATATTTAAGTATACATCACATT
1 AATATTTAAGCATAAATCACATT
17193277 AATATTTAA
1 AATATTTAA
17193286 TACATTTAAT
Statistics
Matches: 136, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 136 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (23 bp):
AATATTTAAGCATAAATCACATT
Found at i:17202810 original size:16 final size:16
Alignment explanation
Indices: 17202789--17202824 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
17202779 GAATTATTTG
*
17202789 TTACAGTTCTATTCTA
1 TTACAGTTCTATTATA
17202805 TTACAGTTCTATTATA
1 TTACAGTTCTATTATA
17202821 TTAC
1 TTAC
17202825 TCTATTCCAT
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:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (16 bp):
TTACAGTTCTATTATA
Found at i:17203058 original size:17 final size:17
Alignment explanation
Indices: 17203038--17203075 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
17203028 CTCCATTGAC
* *
17203038 CTTTAATCTTTCATCTT
1 CTTTAACCTTTCATATT
17203055 CTTTAACCTTTCATATT
1 CTTTAACCTTTCATATT
17203072 CTTT
1 CTTT
17203076 TAACTACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (17 bp):
CTTTAACCTTTCATATT
Found at i:17203063 original size:24 final size:24
Alignment explanation
Indices: 17203018--17203065 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
17203008 ATGGATGTTC
*
17203018 AATCTTTCATCTCCATTGACCTTT
1 AATCTTTCATCTCCATTAACCTTT
* *
17203042 AATCTTTCATCTTCTTTAACCTTT
1 AATCTTTCATCTCCATTAACCTTT
17203066 CATATTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.27, G:0.02, T:0.50
Consensus pattern (24 bp):
AATCTTTCATCTCCATTAACCTTT
Found at i:17208423 original size:17 final size:17
Alignment explanation
Indices: 17208388--17208429 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
17208378 CTCCCTTGAC
*
17208388 CTTTAACCTTCTATCTT
1 CTTTAACCTTCTATATT
17208405 CTTTAACCTT-TCATATT
1 CTTTAACCTTCT-ATATT
17208422 CTTGTAAC
1 CTT-TAAC
17208430 TACTTTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 17 0.77
18 4 0.18
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.50
Consensus pattern (17 bp):
CTTTAACCTTCTATATT
Found at i:17215654 original size:26 final size:26
Alignment explanation
Indices: 17215632--17215691 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
17215622 TTTTTTTAGT
*
17215632 TTTTAAAGGTCCAAAAAAATTTTAAC
1 TTTTAAAGGTCAAAAAAAATTTTAAC
* *
17215658 TTTTAAATGTCAAAAAAAAATTATCAAC
1 TTTTAAAGGTC-AAAAAAAATT-TTAAC
17215686 TTTTAA
1 TTTTAA
17215692 GGGGCTGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 10 0.34
27 9 0.31
28 10 0.34
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (26 bp):
TTTTAAAGGTCAAAAAAAATTTTAAC
Found at i:17222002 original size:30 final size:30
Alignment explanation
Indices: 17221968--17222024 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17221958 TTTGTTTCAG
*
17221968 GTTCT-ATATTATTATTATCTTCTAATACTT
1 GTTCTAAT-TTATTATTAACTTCTAATACTT
*
17221998 GTTCTAATTTTTTATTAACTTCTAATA
1 GTTCTAATTTATTATTAACTTCTAATA
17222025 GCATACCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (30 bp):
GTTCTAATTTATTATTAACTTCTAATACTT
Found at i:17229004 original size:30 final size:30
Alignment explanation
Indices: 17228970--17229026 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17228960 TTTGTTTCAG
*
17228970 GTTCT-ATATTATTATTATCTTCTAATACTT
1 GTTCTAAT-TTATTATTAACTTCTAATACTT
*
17229000 GTTCTAATTTTTTATTAACTTCTAATA
1 GTTCTAATTTATTATTAACTTCTAATA
17229027 GCATACCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (30 bp):
GTTCTAATTTATTATTAACTTCTAATACTT
Found at i:17229515 original size:114 final size:115
Alignment explanation
Indices: 17229331--17229555 Score: 380
Period size: 114 Copynumber: 2.0 Consensus size: 115
17229321 AACTTTGGAT
* *
17229331 ATATTTGTAGAGCAAGCCCAAGAAATACCCTTACTGATTTGCCTTGTCCTCAGGCGAAATCGTGC
1 ATATTTGTAGAGCAAGCCCAAGAAATACCCTTACTGATTTGCCTCGTCCTCAGGCCAAATCGTGC
*
17229396 TTACCACAAATTCCATATACTACAATCTCCCTCTGAGCACAAACCCTGAC
66 TTACCACAAATTCCATATACTACAATCTCCCGCTGAGCACAAACCCTGAC
* *
17229446 ATATTTGTAGAGCAAGCCCAAGAAATATCCTTATTGA-TTGCCTCGTCCTCAGGCCAAATCGTGC
1 ATATTTGTAGAGCAAGCCCAAGAAATACCCTTACTGATTTGCCTCGTCCTCAGGCCAAATCGTGC
**
17229510 TTACCACAAATTCCATATACTGTAATCTCCCGCTGAGCACAAACCC
66 TTACCACAAATTCCATATACTACAATCTCCCGCTGAGCACAAACCC
17229556 CTCGCTATCG
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
114 68 0.66
115 35 0.34
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (115 bp):
ATATTTGTAGAGCAAGCCCAAGAAATACCCTTACTGATTTGCCTCGTCCTCAGGCCAAATCGTGC
TTACCACAAATTCCATATACTACAATCTCCCGCTGAGCACAAACCCTGAC
Done.